I don't think we necessarily need hybrid carriers now that I think about it - In order for them to work, they'd need 3 all new perks that would represent the Hybrid affinities that feel distinct from the ones already present (Autoheal, bonus plane strength, bonus range). As for planes, while I'd certainly like to have them and would download a mod to add them in a heartbeat if necessary, but I'm more concerned with knowing why their missing than demanding they be added, like when a puzzle piece is missing and it's more important to know where it is than to finish. Hybrid victories are more a philosophical point for me, wondering what they would be and how they would distinguish them from their parents. Hybrid cities, on the other hand, are another thing that I'd download a mod for if it's available and not in the base game, but I probably wouldn't really miss it if I had to do without it.
I do think that, with the advent of this uniqueness for the Hybrid units, the original ones need a second look. I agree that all of the 'Ultimate' units should be amphibious, even if it's just the 'shallow' waters and not the deep ocean trenches. What's more, giving the units their unique bonus from upgrading at base would do a lot to bring them more in line, like the Aegis extra attack and ability to move after attacking, CARVR's bonus near a friendly unit, etc... As it currently is, most of the unique units are just better marines that cost a resource, making them lose some of the WOW factor.
Moving them on the tech tree is something I have wanted for a while, since it seems to me that there is no reason to even use the Affinity 9 units given that Affinity 11 are easier to acquire and therefore come faster. Just adjusting where they are so that, generall speaker, you unlock them in the order of the affinity would do a world of good. EDIT: Except SABR. Not sure if it needs moving, but artillery range tends to be good enough for me to warrant considering it later in the game. Again, that's something that it has special though, so giving something like that to all of the units would help.
Finally, one point not mentioned that I would like to see, moreso than hybrid victories or hybrid cities, are hybrid buildings. The units are definitely impressive, and if the nature of hybrid units did not change between now and release, I would personally still be happy with it, but I hope they don't neglect the peaceful side of the affinities. Seeing each affinities spin on the yields, having them value different basic resources differently, it went a long way to defining the affinities as philosophies instead of just mechanics.