I would say this is the age old problem for anything. Many people use this style because it is easy to create. Freelance for it is rather cheap and affordable so it is fairly attractive to indie devs. Just beacuse the previous statement is true deosnt mean its bad or low quality. In fact, many new high end companies are noticing that well done pixel art can be a great way to provide a timeless feeling.
I just recently got into the alpha called: Duelyst and it uses pixel art + new shaders. The art is so well done that I dont even mind the retro freel and at times feel as though im playing with actual models. So, in short, you can do it correctly so long as you put some thought into it.