Judah, Joseph, and Jacob's birthright Jacob had twelve sons, the firstborn of whom was Reuben.  Yet, the birthright that should have passed on to Reuben did not due to Reuben's sin against his father (1 Chronicles 5:1-2).  

Naturally, one would assume that the next in line would be Simeon, the second-oldest.  It did not pass to Simeon either.  In fact, Jacob passes over all of his sons until he gets to Joseph.  

Now, he essentially passes on the birthright and blessing to Ephraim, the younger of Joseph's sons.  

I have a few questions regarding this. 

First, why does Jacob pass the birthright to Joseph's sons, and not Joseph himself?  In fact, before doing so, why does Jacob essentially say that Joseph's sons are now considered to be his sons?  What is the meaning of this?

Second, what is the significance of choosing Ephraim, the younger, over Manasseh, the older?

Finally, even though Ephraim has the birthright, the lineage of Jesus comes through Judah.  Why then, does the birthright not pass to Judah?  Why is there a disconnect between this birthright and the importance of Judah in Jesus' lineage?
Honestly, there are a lot of questions there and rather than skip around I'm going to give one really long background on the birthright and blessing. Just be glad I'm not also giving a treatment to the meaning of firstborn.

There is a TL;DR Conclusion at the end, where I will revisit each specific question.

But first there is a lot of groundwork to lay.

Birthrights and Blessings

First we must understand the meaning of the birthright and blessing.

Birthright gave the son a double portion of the inheritance (Deut 21:17). He also received authority over his father's house and carried the family name. A sort of patriarchal succession. These are very physical, earthly rewards.

The blessing is a bit less specific and often varied. But the first blessing always seems to be the greater. It also often has prophetic meaning, though the people at the time probably thought of it the other way around. That receiving a good blessing ensured the future it promised. They may have physical results, but the giving of the blessing is spiritual in nature.

Covenant with Abraham

There is a third aspect here, however, specific to Abraham's family: God's covenant with him.

Along with the land of Canaan and a promise to be the God of his children, God promised Abraham (Gen 12)


Great number of descendants (Physical)
All the families of the world be blessed through him (Spiritual)


Isaac

Isaac was recognized as Abraham's firstborn, though Ishmael was technically first, but not God's firstborn.

God pledged to establish this same covenant with Isaac specifically in Genesis 17:21, thereby leaving Ishmael out (though Ishmael does receive a lesser blessing of his own).

God also then gives Isaac a blessing when Abraham dies. Whether this was a separate blessing unique from God or this was God honoring the blessing Abraham passed to him, we cannot know for sure. Gen 25:11


  After the death of Abraham, God blessed Isaac his son.


Jacob

The pattern continues with Isaac's sons, Esau and Jacob, with Esau as the firstborn.
However, God told Rebekah that the younger would serve the older, implying that the younger would receive the birthright and/or blessing. Gen 25:23

Jacob, in fact, does get both the birthright and the blessing. This is where we first see the birthright and blessing clearly distinguished.  Esau sells his birthright, and is later cheated out of his blessing and refers to them both as separate things. Gen 27:36 


  He took away my birthright, and behold, now he has taken away my blessing.”


This is also the first time the Covenant has had two legitimate sons to pass to, but instead of passing to Esau or to both Esau and Jacob, it goes solely to Jacob.

Which begs the question:
Did Abraham's Covenant follow the birthright or the blessing?
Or is it both or neither one? Well let's see:

This is Isaac's to blessing to Jacob. Gen 27:27-29


  “See, the smell of my son
  is as the smell of a field that the LORD has blessed!
  
  May God give you of the dew of heaven
  and of the fatness of the earth
  and plenty of grain and wine.
  
  Let peoples serve you,
  and nations bow down to you.
  Be lord over your brothers,
  and may your mother’s sons bow down to you.
  Cursed be everyone who curses you,
  and blessed be everyone who blesses you!”


Emphasis added by me. Do those parts sound familiar?
Genesis 22:17


  I will surely bless you, and I will surely multiply your offspring as the stars of heaven and as the sand that is on the seashore. And your offspring shall possess the gate of his enemies,


Genesis 12:3


  I will bless those who bless you, and him who dishonors you I will curse, and in you all the families of the earth shall be blessed.”


Also in this blessing we have bountiful wealth and the authority over his family.
So we see the birthright AND elements of Abraham's covenant being passed in Isaac's blessing.

Jacob later receives a renewal of Abraham's covenant from God himself (Gen 28:14)


  Your offspring shall be like the dust of the earth, and you shall spread abroad to the west and to the east and to the north and to the south, and in you and your offspring shall all the families of the earth be blessed.


So Jacob receives four promises:


Double inheritance from Isaac (Birthright)
Authority over his father's house. (Blessing and Birthright)
Descendants/Fruitful (Blessing and Covenant)
Bless the nations (Covenant


Quite the haul! So we see Abraham's covenant following those who receive both the birthright and the blessing in the cases of Isaac and Jacob.

Jacob's Sons

Judah was the fourth born son, but due to his older brothers Reuben, Simeon and Levi's failures he rose to the top of the legal "firstborn" rankings. (Genesis 34:25, 35:22)

Meanwhile, Joseph was given visions by God showing him that his father's household would bow down to him. Which his brothers clearly understood as a claim to the birthright's authority. However, Jacob takes note that it isn't just the brothers bowing to Jospeh but Jacob as well! This is highly unusual, for the authority of the birthright has not superseded the father's before ("mother's sons will bow").

It ends up making sense though, as Jacob and his household do end up bowing down to Joseph in Egypt under entirely different circumstances than they could have ever expected. So it seems the vision was not speaking of the birthright's authority, but was only prophetic of Joseph ruling in Egypt.

Then at the end of his life Jacob summons Joseph and his two sons, Manasseh the elder and Ephraim the younger (Gen 48). Jacob declares that they will be counted as his own sons. Not just as his own sons, but as Reuben and Simeon are. Remember who Reuben and Simeon are? The oldest two sons!

Jacob is not just adopting them into his inheritance, he is proclaiming them to be counted as the eldest! This detail is often overlooked (1 Chr 5:1)

Jacob continues on to give them their firstborn blessing, but not satisfied to have upset the normal order just once in placing them ahead of Reuben and Simeon, he crosses his arms and places his right hand on Ephraim, the younger!

First, Jacob proclaims a blessing over Joseph, which we can understand as both sons: Gen 48:15,16


  15And he blessed Joseph and said,
  “The God before whom my fathers Abraham and Isaac walked,
  the God who has been my shepherd all my life long to this day,
  
  16 the angel who has redeemed me from all evil, bless the boys;
  and in them let my name be carried on, and the name of my fathers Abraham and Isaac;
  and let them grow into a multitude (or fullness) in the midst of the earth.”


Which of the four that Jacob received do we see here?


Many descendants


I will also note that Jacob says "in them let my name be carried on, and the name of my fathers Abraham and Isaac".
It is speculation, but one can say at the least that this ensures their inclusion as equal sons and future tribes of Jacob/Israel. One could also take it to be prophetic in that the name Israel does very much carry on in Ephraim and Manasseh throughout history. Even during David's time, before the division of the kingdom, the army of the north, led by Ephraim, are called the army of Israel, while the army of the south is the army of Judah (1 King 2:32). And of course, when the kingdom is divided God says to Jeroboam the Ephraimite that He is going to be "king over Israel" and indeed the northern kingdom keeps the name of Israel, apart from Judah (1 King 11:37)

Finally, Jacob turns to bless Ephraim and Manasseh specifically, giving Ephraim the greater blessing, a prophecy of becoming great nations (Gen 48:19). Thus Jacob reinforces that while both will receive the blessing from Abraham's covenant, Ephraim receives the first and greater share.

Now Jacob gathers all his sons and gives each their own blessing, as we saw Isaac still give Esau his own blessing apart from Jacob. He gives the blessings in order of birth, not importance.

Judah is given a unique blessing in Gen 49:10


  The scepter shall not depart from Judah,
  nor the ruler’s staff from between his feet,
  until tribute comes to him;fn
  and to him shall be the obedience of the peoples.


Judah appears to be given the authority to lead. 1 Ch 5:2 affirms that though Joseph received the birthright, Judah lead the nation.

Then Joseph receives his blessing which once again affirms descendants, fruitfulness, and the blessing of God.

The Breakdown

So let's check the score:

Joseph


Fruitful Inheritance, Double Portion in Two Tribes - Birthright (Jos 17:14-18)
Great Descendants - Covenant (Also Jos 17:17)


Judah


Authority - Birthright


There is only one part missing, that all nations will be blessed through him.

Peter identifies the link in Acts 3 and Paul agrees in Galatians 3 that it is Jesus Christ, the Son of God, the Son of David of the tribe of Judah who has both received the ruler's staff and in whom all the families of the earth are blessed.

TL;DR Conclusion


  First, why does Jacob pass the birthright to Joseph's sons, and not Joseph himself? In fact, before doing so, why does Jacob essentially say that Joseph's sons are now considered to be his sons? What is the meaning of this?


As I hope to have displayed above, Jacob adopted Joseph's sons as his own and as his firstborn. As for why, we can't be sure, but by doing so and by counting each as full fledged sons, he ensured Joseph received the double portion (one in each) of the birthright. Joseph is 11th in line to be the physical firstborn, but Jacob chooses him above the rest.


  Second, what is the significance of choosing Ephraim, the younger, over Manasseh, the older?


God chose Ephraim just like he chose Isaac, the son of a free woman, over Ishmael, the son of a bondservant (Gal 4). Just like God chose Jacob over Esau before he was born (Romans 9). Ephraim is God's firstborn (Jer 31:9) not man's. This is seen by the New Testament writers to show how God chooses who he wills and that he can adopt anyone as his son or daughter regardless of our physical state of birth.


  Finally, even though Ephraim has the birthright, the lineage of Jesus comes through Judah. Why then, does the birthright not pass to Judah? Why is there a disconnect between this birthright and the importance of Judah in Jesus' lineage?


Joseph is said to receive the birthright, but it is clear he does not quite get all of it. Judah receives the authority. Whilte Ephraim and Judah were the two alpha tribes of Israel , chiefs and later kings came from Judah. (1 Ch 5:2)

Jesus does come from the line of Judah, one cannot help but believe it was for David's sake (2 Ch 21:7). Whether that means God knew David would come from Judah, or whether David was who he was (a king) only because he came from Judah is up to the reader.

Ephraim, through Joseph, receives the double portion half of the birthright and the great descendants half of the Covenant (same as half the Blessing if you agree that the Covenant follows the blessing and birthright). Ephraim is God's spiritual firstborn (Jer 31:9) like Isaac and Jacob were, despite not being physical firstborns according to law.

Judah receives the authority half of the birthright and the half that blesses all the families of the earth through the Covenant. He is the physical firstborn according to law.

The spiritual and physical parallelism of Ephraim and Judah is quite evidence. Judah physically provided, or delivered, the source of blessing in Jesus and Ephraim displays God's ability to spiritually adopt and bless firstborn children from among all the families of the earth through him.