Theories are fun. I think I’ll mess around with this hypothetical concept a little bit.
Well, the biggest thing that comes to mind is Makoto’s dash. In general, 3rd Strike characters had considerably faster dashes and backdashes than characters in SF4. This is a big deal for Makoto in particular, who had the fastest dash in the game (and the second fastest backdash next to Oro, although it didn’t go very far.) I imagine this was a particularly difficult balance question for the SSF4 designers because dash speed and properties happen to be such an important part of SF4’s system due to FAs and FADCs.
I don’t think her dash will stay the same speed, but unless it is heavily reduced, which seems unlikely, she’ll have very strong FADC combo options. I wouldn’t be surprised if she could just do a straight non-juggle FADC -> Ultra 1 from one of her specials. If Makoto can FADC a launching move like EX Hayate, or if Fukiage can hit standing opponents now, FADC -> Fukiage -> jump-cancel Ultra 2 should be possible. And outside of combos, a blocked FADC’ed special might give her decent frame advantage, as might a blocked FA canceled to dash. Both of those should help her pressure game.
As for non FADC combos, as posted earlier, Fukiage jump canceled to Abare Tosanami would make sense (or maybe a high-enough Tsurugi?) … Now, if I were to make a guess, there are two lines of thought I can follow here. In 3rd Strike, even though it was a super, Seichusen Godanzuki had a fair number of links into it, but that had to do with supers being quick and moves (Makoto’s, but in general also) having more active frames and less recovery frames. Abare Tosanami was harder to combo into and relied on your ability to consistently land Karakusa. The other part of that is that using Abare Tosanami used to allow more access to EX moves since you had 2 super bars.
If they wanted to transfer those differences to the SSF4 ultras, they could follow similar patterns - give Ultra 1 combos from more varied sources that perhaps cost more meter most of the time, but have less utility as a raw punish due to its range, and have Abare Tosanami rely on one or two specific combos (cheaper ones meter-wise so you feel more willing to spend meter on EX moves) but allow access to the post-ultra juggles and bonus usefulness as a deterrent against fireballs, dash punches, and so on.
And we still don’t really know what exactly EX Karakusa is for, so who knows what could happen there.