Concerning the "teenage protagonist" problem: Think of most of the popular anime coming out of Japan. What do a lot of them involve? Schoolkids going through all kinds of issues. And the audience just eats it up, regardless of the age bracket. So of course, most video games will go for the lowest common denominator when it comes to plot and characters. that's why we still have little girls with annoyingly high voices running around killing things.
Oh yes, that's one thing that annoys me. Characters (main or otherwise) that have to be as exhuberant and obnoxious as humanly possible in an effort to sound "cute" or "passionate". And that concerns both english and japanese voice overs.
Romantic <insert geometrical nightmare here> - Don't get me wrong, I like a romantic ploy in an RPG. But when you get the typical "mother hen vs. every other female" thing, I tend to want to shoot things. Atelier Iris' Lita annoyed me to no end regarding that, especially since she then tried to play it off like she wasn't interested in Klein.
One thing I applaud Skies of Arcadia for NOT doing is pitting Aika vs. Fina for Vyse's affection. Yeah, there were signs that both girls were interested in him, but there were bigger things at stake than shagging the guy. This is one of the things that worries me concerning Wild Arms: Vth Vanguard, since it has a similar setup with its main characters (main character/childhood friend/mysterious girl).
Another triangle I think was handled well was Grandia II's Ryudo/Elena/Millenia. Nothing beats a schizophrenic priestess being possessed by a psychotic demonic redhead.
I also admit to getting weary of the whole "weak healer/magic user female" thing. Those types always seems to get the soft, submissive personalities. I want a pyromaniacal psychoslut with homicidal tendencies, dammit! One who can wield both powerful magic and powerful weapons! I haven't played much of Dragon Quest VIII, but Jessica is a good start I think.
And I'm also sick of the "giant, 30-story tall alien blob as the final boss" shit. There are things far scarier than that these days. If J. Edgar Hoover is trying to destroy the world, then I want to kill J. Edgar Hoover and be done with it, not have to move on to fight the Stay Puft Marshmallow Man.
And crappy music. I can handle long dungeons, tedious battles, and monotonous minigames as long as the accompanying music is a good listen. Crappy music makes playing even the good games tedious. at times. Shadow Hearts; Covenant is a big offender there...fucking Idar Flamme and it's wannabe "scary movie" music...
I'll shut up now.