It's a method of balancing. I don't particularly care for it myself, feels like this game is often more about running your own stuff then having to respect what your opponent can do to limit your options. It seems really hard to get opponents to respect anything in this game due to the amount of options.
Hmm... I don't really get this feeling. I think a good assist or 2 can really mess with the playstyle of people in this game, and, ESPECIALLY this early on, people don't have a variety of styles to use.
Early on, I used Cerebella with her Excellabella AA throw as Assist, to back up Parasoul. Every Valentine, Filia, and Ms. Fortune was royally screwed if they didn't change their IAD styles, as the move would totally eat it, and give me enough time to dash to the other side of the screen, and prep my punishes. (Still love using it now, too fun an option, but I don't depend on it as much.)
And then take the example of the "OP" Double assist. An assist that has the same Startup-vulnerability as all assist in this game, can be ducked at near mid-range, and at far range, leaves her 100% open to punishes. Once people get used to it, it'll be natural, but for now, it forces people to play in a style they don't know yet.
Personally, I find it GREAT that each character has a way to deal with everything (zoning, rushdown, turtling, etc) within their arsenals. It means that if you're losing to something, it's YOUR fault, not just some crappy tiered design philosophy.
The fact that almost ANYTHING (throws, assist, an IAD overhead, etc) can lead to extremly strong combos / resets in thsi game, leads me to feel that respect for ones options, moves, and playstyles will come naturally once everyone is comfortable with the game as a whole.
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Personally, I really love the fact that I don't HAVE to play certain characters to get the assist I want, due to these custom assist. I really liked Captain Commando in MvC2, and the closet I could get to CapCorridor in MvC3 was with Dante, a character I have no desire to play. Not a prob in this game. And the fact that there are no 100% invincible assist is also very nice; Every assist has clear weaknesses, uses, and ability to be punished.
The balance in the ratio system here is also nice. Unlike Mahvell, where I feel as if having a 3 man team is all about making 1 character strong (and playing 2 assist charas with moves you like... which might be with characters you DON'T), I feel that I can go tornado-tag, with 2 characters I'm equally good with, or KoF style "Every character is my main!" with 3 man teams, in this game, and still have a shot. And actually have FUN with it, because, y'know, my characters are all actually made well enough to be WORTH playing. I don't even feel that mad when a ration 3 (solo) kills off 1 of my ration 1 (3 man team) characters... I rarely ever feel like I lose my way to win in this game, even in desperate situations.
And it's suprisingly un-lopsided, which amazes me, given the options. I can play as a 3 man more-KoF style (each chara is an equal threat, Battery/2nd main/primary main team), and an opponent can play the 3 man more-MvC style (An uber character with 2 awesome new specials), and both ways seem to have mostly equal chances at success.
I'm finding I'm a real fan of "Make the characters well, and let the underlying systems balance them out!" in fighters. It really helps to open up a wider portion of the cast to being REALLY viable, and enjoyable to play. Seems like it was a really smart choice (among many) for SGs.