Why compare SE's output to Capcom's?
SE's Crystal tools was the first time they ever made their own inhouse engine intended for HD and dexterity as opposed to making a single purpose engine for every single game. And they admitted it was a nightmare based on the fact that they were designing the engine as they were working on XIII, making the engine fit to what they wanted to do with the game instead of the other way around, hence crippling their output for the rest of the gen(XIV1.0, XIII-2, XIII-3 ect)
In comparison, we have Capcom who have already invested heavily in making multi purpose engines like MT Framework and the Taito board system, which work well and have served their purposes in multiple games.
Its like comparing apples to oranges.