How come it's actually Black with the advantage here? I was analyzing a recent game of mine, and I noticed something interesting. After I blundered back a bishop on move 16, the evaluation was -3.4, which is still strongly winning for Black.
[White &quot;White&quot;]
[Black &quot;Black&quot;]
[Result &quot;0-1&quot;]
[WhiteElo &quot;1700&quot;]
[BlackElo &quot;1500&quot;]
[fen &quot;&quot;]

1. e4 c5 2. f4 { B21 Sicilian Defense: McDonnell Attack } b6 3. Nf3 Bb7 4. Nc3 a6 5. Bc4 e6 6. O-O d5 7. exd5 exd5 8. Be2 d4 9. Ne4?? { (-1.03 → -4.31) Blunder. Nb1 was best. } Bxe4 10. d3 Bb7 11. Ng5 Be7 12. Bf3 Nc6 13. Re1 Nf6 14. Qe2 O-O? { (-5.42 → -3.17) Mistake. Qd7 was best. } 15. Bxc6 Bxc6 16. Qxe7 Qd5 17. Nf3?! { (-3.25 → -5.04) Inaccuracy. Qe2 was best. } Rae8 18. Qc7 Rxe1+ 19. Kf2? { (-4.63 → -19.29) Mistake. Nxe1 was best. } Ree8 20. Qxb6 Ng4+ 21. Kg3 Ne3 22. Qb3 Nf5+ 23. Kf2 Qd7 24. Bd2 Bxf3 25. gxf3 Nh4 26. c4 Qh3 27. Qd1 Qxh2+ { White resigns. } 0-1

How is this so, given that the material had evened out? Obviously, if it's not due to material, it must be due to something positional, but even then I'm not very convinced. After move 16, White owns the e-file and maybe even the 7th rank. They also has a knight on g5 which, to me, is a bit worrisome (should it not be?), and it's supported by a pawn and a bishop. What merits such a strong evaluation for Black?
White's actually quite close to busted in that position after 16...Qd5. Of the two points you bring up, note that White doesn't actually control the e-file because Black is ready to play a rook to e8 and drive White's major pieces away. The knight on g5 looks good, but it's also vulnerable to being kicked by ...h6 and it's not threatening anything yet. Otherwise, White's king is dangerously exposed on the long diagonal since Black already has a bishop on the diagonal and since White no longer has f3. Finally, White's queenside is undeveloped. Granted Black's a8-rook isn't developed either, but it can jump into the fray much quicker.
Consider, checkmate is threatened on g2 and White has only a few ways to defend it:

17.Re2 is the easiest to refute because 17...Rfe8 wins either a rook or the queen.
17.Nf3 is also terrible. Again Black plays 17...Rfe8, and after 18.Qc7 (or where else is White going to put the queen?) Black plays 18...Rxe1 19.Nxe1 (forced) 19...Rae8 (developing with tempo) 20.Nf3 (still forced) Re2. Black's pieces are overwhelming White's king while White's queen, bishop and rook are all spectators. An immediate threat is 21...Rxg2+ 22. Kxg2 Qxf3 and checkmate.
That leaves 17.Qe2, which is the least evil but still not good enough. Black again plays 17...Rfe8, forcing 18.Ne4 (all other moves either lose material or get mated on g2), and then the Knight is pinned. Black has a variety of promising ideas such as 18...Qf5 intending to take on e4, or 18...Nd7 intending ...f5 to win material.

By the way, it's striking how much of Black's advantage stems from the fact that White's queenside is undeveloped, and by extension the rook on e1 is undefended (once ...Rfe8 kicks the queen away). Move White's c1-bishop to d2, and Black's advantage drops to about -1.0.