I used to play a lot of Doom when MvC3 was new, and I've played a hell of a lot of Akuma; I don't think the two go well together. Maybe if one was on point, and the other was the anchor. Akuma 2nd with Doom missiles as anchor would work, but I'm not a huge fan of missile assist, because against some teams, it destroys them, but against others, that assist is either useless or gets Doom killed.
I'm testing some combinations between the four characters you mentioned, and I'd probably go with Skrull, Nova, Akuma (or Doom rocks anchor you really want Doom).
Rocks can help skrull do random special dives (generally) safely, and centurion rush sets up near unblockables with skrulls down+H dive (not a true unblockable, assist always hits first, but by a fraction of a second) although you need to be near corner to continue the combo. Rocks are a bit slow for Nova if he's rushing down, but tatsu assist is great with Nova. It's also good for skrull who can also easily dash forward for launch combo if tatsu assist hits. It locks them down for command throw mixups, or can help protect command throw attempts.
Helps Nova in a similar way, locks them down for instant overheads or lows, he can airdash from midscreen when calling tatus assist and end up behind the opponent.
It depends a lot on how you play each character. Who are you most comfortable with as an anchor if they didn't have xfactor? Unless the assist is REALLY good, I think this is pretty important.