Some of it comes down to taste certainly but I stil think theres an argument to be made that the kind of cutting edge stuff that was allowed to make it into the mainstream in Japan at that time represents distinctly identifiable period (if peak is too strong a word because $ and volume of output has gone up as you point out.) kind of like how in the us were seeing articles asking why hollywood made The Matrix in 99 and a million comic sequels today, Japan bloggers are wondering why One Peice and Idol groups dominate?
I agree with you that the output of the 90s represents an identifiable period in Japanese pop culture, but don't agree with the original sentiment of things having necessarily "stagnated" since then. There may be an argument, as you suggest, that the period was more progressive in a sense, but I'd have to see more examples of what you're talking about before I could agree.
The dominance of things like One Piece or AKB48 don't preclude the creation of "cutting edge" stuff, though they might certainly drown those out and make them less visible. I think something similar could be said for the 90s, with the popularity of Dragon Ball and Morning Musume, for example (though to a lesser degree). Still, the Internet has allowed for the creation and popularity of lots of interesting stuff, even if they may not be "mainstream."
