PhoenixWright: Is it? Or are you glazing over Barbie's Horse Adventures while not giving indie games the same much needed slack?
EDIT: This isn't meant to be a snarky one-sentence retort, my point is just so dead-simple (and very possibly off-base) in this case...
StingingVelvet: I give indies slack all the time but they still mostly come up short. Even with all the flaws and mass-market pandering of a game like Dragon Age 2 I would still rather play that than your typical indie game. That's just me, and given sales figures most other people, but not everyone of course, which is fine.
I do love some indies. Super Meat Boy is amazing, Castle Crashers, Amnesia... there's a long list. On average though when I buy something like a Humble Bundle or a cheap indie RPG on Gamersgate I end up never playing them because they just really aren't that good.
In general I'd agree with you that indies are typically worse than professional games outside of the niche market they specifically cater to (usually the one the author belongs to).
In the case of jRPGs, though, I'd say that some of the indie ones like Cthulhu Saves the World are much better than anything professional Japanese companies like Square have made recently, at least for people who like the classics of the genre.
That being said, while RPGMaker games can be good, I typically wouldn't pay for one considering that even if you like them, you can in my opinion find some free ones that are as good or better than the ones being sold on GG or Amaranth.