I think it's interesting megatronx that you say retro games are "fun, fast, challenging and simple to control" - none of them are attributes specific to retro games - non-retro games can be all of those things too.
While it's true that they can be, and some actually are, it's a gap that seems to be getting wider as time goes on. Like Mipey said, it's a bloat issue.
I also see many nuschool games that look absolutely amazing, but have gameplay and design flaws littered throughout. Clunky interfaces, odd controls, glitchy movement, or are just flat-out buggy. It's like they're holding the content in higher regard than the core... polished turds, in other words. Games with no soul.
I believe it's because developers are spending so much time and money on the content that the core gets neglected. This is especially true with the movie tie-in games you see (but then again, movie tie-ins have always suffered from this).
I also think that games in general just aren't as "pure" any more. Again, because companies spend so much on the content the want you to see all of it. What you end up with is one long tutorial that holds your hand through the entire game. As an example of a "pure" game, I'd cite the original Metroid for NES... it was just about perfectly balanced as far as challenge goes. It didn't hold your hand at all... it was just you vs. the game.
One last thing I've noticed about retro styled indie games vs. hi-res indie games... the retro styled ones are almost always more "forgiven" by critics and the general public. The more polished your game is, the more likely people are to nitpick at it. For example, Eternal Daughter is lauded as one of the best indie platformers in recent years. It has a pretty large fan base... just about anyone who plays it is satisfied. Aquaria, on the other hand, has a disproportionate number of detractors. It was made by the same person, and was even billed as "the spiritual successor to Eternal Daughter." By all rights is a far superior game as far as the art, technology, depth of gameplay, etc. are concerned. And even though it's seen it's fair share of success, you will find that a larger percentage of people who've played Aquaria as opposed to those who played Eternal Daughter didn't like it or complained about it's flaws. I believe it's because the closer you get to "professional," the less forgiving people are in regards to your game.
It could be that you get more complaints for a paid product than you would for a free one, sure... but I don't think it's just that. I think people are just more willing to overlook a game's flaws if it's presented in a more "home-made" or "lo-fi" way.
Or it could be that fancy looking graphics just get your expectations up about a game more so than lo-fi graphics. You expect the gameplay to be as amazing as the visuals, but that rarely turns out to be the case, and so you end up disappointed.