I think the problem is companies are trying too hard. On 3d games you HAVE to innovate, because, quite frankly, your average 3d game totally sucks. The genre is too new and thus much improvment can be made. 2D games are a different story, they have been around so long and have been refined so much, that a developer really has to do is make new levels and a new story.
I think the best example of this "trying too hard" thing is the megaman series. They have released around 30 megaman 2d games in the past couple of years. All but the latest totally sucked. Why? Well they tried to re-work megaman in each game they did, adding lame gimmicks, lame storylines coupled with major graphical overhauls. Unfortunately with all the reworking someone forgot to tell capcom that megaman is all about the jumping and shooting. It's also about levels that are so tweaked to the jumping and shooting that it is a thing of beauty.
Now the most recent game is really good. Why? Cause they basically just prettied up the original megaman engine. With classic megaman platforming you can never go wrong.
Same goes for franchises like castlevania, metal slug and mario bros. Don't worry about innovating, spend all of your time working and re-working those levels and making sure the gameplay mechanics match the original. THEN go back and overhaul the graphics and add in any special do-dads you have time for.