Why are almost all indie games 2D?

I'd much rather have quality game play, than fancy graphics. I actually hate it when people make games 3D that don't need to be. For the same development time, you'll get much better graphics with a 2D game than a 3D. As to why a there are a lot of 2D RPGs that all look the same, it's because a lot of them are made with the same tool set, like RPG maker.
I know it may seem easy, but 2D development isn't simply a walk in the park. Pixel art does take a lot of work to look "just right" and encourage you to use your imagination to the details that aren't there. Of course everything art related is opinion, but there is "bad" pixel art much like there are bad 2D art and bad 3D art.

You got to remember there is passion into making a game. Independent developers (small and large scale) want to make games they've enjoyed and still enjoy with hopes you will enjoy them too. Budgets also factor into the scope of the game.