I just remembered one BIG pet peeve... even if it will probably get me labelled a conspiracy theorist.
The loss of confidence among Japanese developers.
I'm inclined to place most of the blame for this on American gaming sites, particularly since a lot of gamers (and especially newer gamers) tend to parrot what these sites promote. I remember seeing signs of anti-Japanese sentiment creep up toward the latter half of the last generation, with games like God Hand being horribly misinterpreted and misrepresented, but it's only magnified since the start of this gen.
Part of it stems from the open opportunity presented, in that every time a new generation rolls around, the first wave of games is always the among the worst. Graphics are a bit rough, mechanics are a bit rough because developers were focused on just getting shit to work at all and under a tight deadline, and so on. Since Japanese studios typically have less money to throw around, it often takes longer for them to hit their stride. Others, like Atlus, take over a year to really find a comfortable point, as they're still transitioning from their release schedule of stuff for the previous systems.
As US studios hit that stride much earlier, the American media seized on the Japanese. JRPGs were all suddenly not "fresh" enough and were almost guaranteed to hit around a 5-6.5 review score, shmups were suddenly "dated" and "too easy" because they weren't all made by Treasure, and the rare oddity like Dead Rising was considered a fluke of sorts.
That pessimism eventually translated to poor sales figures, and suddenly everyone - including Japanese publishers and developers - decided that the whole industry over there was dead in the water. It suddenly stopped being OK to make Japanese-style games, and it became some kind of ridiculous mandate that if a Japanese game is ever going to succeed, it has to appeal to Western tastes... nevermind that not so long ago, games like Final Fantasy VII and Persona 3 appealed just fine to "Western tastes." So studios started farming work out to non-Japanese studios, and - surprise! - the results were often far worse than anyone anticipated (and we all have examples of this, I'm sure), which just further reinforced the image that Japanese studios are clueless and have nothing to offer.
I'm not saying that the JP games out this gen are the best ever, and there are obviously exceptions (Dark Souls, Catherine, etc) but there is a massive disparity between how Western and Eastern games are being scored, marketed, and distributed, and it's fucked up when pretty damn enjoyable JP games are getting marked at a 5 for not being "innovative" or flashy enough, even though most of us could likely point to dozens of US-developed games that are horribly half-assed and unoriginal, yet continue to garner at least an 8.0, if not higher.