Certainly, I think lot of it is to do with the designers graphical abilities, or at least the time it takes to produce them.
For a while I thought I was alone in that thought. Phew.
With a limited indie budget (usually consisting only of allocated TIME) one has to choose carefully. Since gameplay is what really matters, graphics usually get a big cut (and audio too).
I did release some unfinished work here (rocket-days) with fullscreen effects (two alpha blended layers) and whatnot and was told that it ran too slow and I should take em off.
Also, there's the long-standing argument over motion blur.
I'm all up for stunning 2D look. Scaling up is not really an issue (unless that bug of enlarging window still remains ) as there are tools to scale to any resolution. Of course it doesn't improve as 3D does, but it's just as it would look on the original resolution but with better edges.
All that said, once you go commercial people apply commercial standards, which are running sky high.