My friend says the AE upgrade really set SFIV back(such as zoning being nonexistent). What, exactly, changed about how the flows?
To be frank, your friend is stupid. Super already made zoning extremely difficult because of all the fireball-invincible moves the game has. The problem with Super is that all the top tier ended up being almost all charge characters as a result which made the game extremely slow and boring. AE still puts a stronger emphasis on characters with strong footsie tools, but now at least not all of the top tier are charge.
People cry about the twins a lot, but really it's just everyone being whiny bitches. Yun needs some tweaks on his wake-up options and damage output, but the biggest problem with the twins is the fact that they have a fast and throw-invincible command throw. Fei Long is strong too, but that's just because of his design for the most part. Rekkas are very strong in games that are footsie-intensive, like AE is.
Uh, the biggest problem about the twins is that they get in almost for free and they have safe braindead offense. Super was still a mutch better game, and there were plenty of strong offensive characters like Cammy (top 5 in Super), Abel, Akuma and Rufus. Super was a game where any playstyle was good enough to win, be it rushdown, zoning or footsies. People complained that it was slow because usually those that were impatient lost to players that were. In AE It's all about braindead safe offense (Viper, Twins, and to a certain extent, Fei) that's easy to get going and that you can't really do much to defend against.