Matching your genre to your artistic style is a problem. But I do think that the guerilla nature of indie publishing and online publishing will shake up the old concepts of covers and genres.
For me it's a major problem that I write light or "cozy" mysteries, but neither my books nor my covers fit what is currently in vogue. My one series would probably do better if I could do a modern style "cozy" cover, but it would be costly. The issue is that cozy mysteries always have a quaint painting of a domestic setting, with a murder element in it. I don't do that kind of art, and it really is something you'd have to commission.
My solution to the problem was to look back at the kind of mysteries that I admire, and which I use more for inspiration for my work, and go with a retro style. I came up with a design that evoked Saul Bass and also the logo for The Saint (who the title character is compared to here and there, though he has his doubts). I ended up winning an award for the cover, but until I get more books out in that series, I don't see it helping me much.
(If you want to look at it: http://www.amazon.com/dp/B006RPUHMI/ )
I think creating my own brand -- using my own artistic style -- slows me down, but I think it will pay off in the end. When I think about well established authors, often their series are treated differently than the run of the mill books (at least in mystery). Look at the cover of an Agatha Christie, and you'll find it doesn't fit the model for most modern cozies. (But then, her work doesn't either.)
I think it's going to be tougher in your area, in sf/fantasy, because the fashion is moving from an expensive style (painting) to a quicker more graphic style. So painting is going to look "old-fashioned" for a while. In ten years, though, it will look retro and classy. However, I expect that just using a different kind of painting, a different look, than sf and fantasy has used recently (maybe more fine arty?) that would stand out and not be against you.