Calling Ars Magica an "indie" game is like calling one of Spielberg's movies "indie" because he happened to have used his own studio instead of Paramount.
...if we assume that it was Spielberg's first movie and he made it out of his garage on a shoestring budget, sure. And, yeah, I'd call that an "indie" movie. Nobody starts off as one of the big names. Spielberg didn't, and neither did Tweet or Rein*Hagen.
Speaking of VB -- perhaps you can help me on a couple of things:
I've looked over a few of his games, and the vibe of them just loses me. Don't get me wrong - he's a good writer, and he definitely has clear vision for his games .... they all just seem a little too Mary Emo-Sue for me -- it's seems like he grew up under the tutelage of White Wolf, and then turned it up to 11. Is that what you mean by "cup of tea"? Also, I don't like how vague the settings and GM section are. It just doesn't seem like a whole stand-alone product to me. If there is going to be that much left up to user input, then charging me that much ('cause VB does have a relatively high price point for his stuff) is rather insulting -- don't fucking charge me for MTP.
High price point is the bane of indie games; when you're printing 500 copies, you can't get the same rates as someone who's printing 5,000.
And, yeah, that's largely what I mean by "cup of tea," though I wouldn't exactly describe DitV as "emo." Baker does tend to focus heavily on the psycho-drama, but there's a lot in there I think is of merit. He's not the only person to structure games in a style that's explicitly episodic, rather than linear, but he does a good job of laying out the reasons for structuring the game that way. (Mind you, I'm biased--I happen to think tabletop RPGs work better in an episodic format.)
I generally put indie games (at least as they tend to be defined today) in the same category as, say, stream-of-consciousness writing a la Joyce or Faulkner. It does new things, a lot of more mainstream writers may be inspired to incorporate some of those new things into their own writings--but not really what the typical reader wants to pick up and read. Thomas Pynchon would be another great example. The large majority of readers tend to give up on it afer a few chapters, because it's so frigging inaccessible. On the other hand, there are a lot of writers out there who have been influenced by the book, and that influence shows up in their own writing, which is more accessible.
I'd argue that the main impact of good indie games on the RPG industry as a whole is like that. You're never going to see DitV or Sorcerer or SotC become a competitor to Pathfinder, but you
will see concepts from those games popping up in Pathfinder and similarly-popular systems.
A lot of these games (i.e., indie games in general) have this free-form thing going on; and to me, this just comes off as being lazy with your system. You can tell that a lot of these are made with a very particular play style (not just game style) in mind .... like the game(s) was custom-made just for this guy's own personal play group -- which is just rather myopic, IMO.
Depends on your design goals. If you want to become a rich, famous, and successful game designer, then yeah, it's absolutely myopic. (Mind you, I'd also say you've taken some pretty good drugs, since becoming a rich, famous, and successful game designer is about as likely as becoming a rich, famous, and successful breeder of pedigreed show hamsters...but I digress.)
On the other hand, if your goal is actually to say, "What can be done with the RPG medium that hasn't been done before?" then you have to be prepared to accept the fact that a lot of what you try is going to just outright fail, and a lot more of it is going to leave many people scratching their heads and saying, "Huh?"
Pretentious? Maybe. I'll admit, my own RPG writing tends to be about as mainstream as you can get; I'm aiming for clean, comprehensible, and fun, not for groundbreaking art. On the other hand, I've seen some damned good ideas pop up even in indie games I otherwise considered pretentious crap.