There is one thing about the order in which the units are numbered that strikes me as awkward. I keep thinking that keys 1-4 will select my mantas, and I can't really seem to get used to it being 2-5. From having the fingers on the WASD keys it is quite easy and convenient to reach 1-4, but 5 is a little bit off. I often hit the 1 key when I wish to quickly select my first manta to send it in for close air support, but end up with the not very useful (for the situation) carrier. My brain still thinks of them as manta 1-4. Maybe the original game is just too solidly imprinted in my brain.
I could easily live with the carrier being selected with 9 or 0. It has never been that urgent to select the carrier that I don't have time to look down at the keyboard to find the key. The tilde key would of course work fine too. Also I think it is kind of odd that the name of your first manta is manta 2. Then there are the walruses with the names 6-9. That doesn't bother me as much for some reason, but I still wouldn't mind hearing them called walrus 1-4, and maybe be selected with the F1-F4 keys.
This is not exactly a game breaker or even a huge issue, but after having spent several days with the game, it remains awkward.
Am I the only one thinking this?