We can really assist with your specific theme-NextGEN conflicts above. The lower resolution problem of NG featured images is well known, though, and there are a number of other issues with Featured Images and NextGEN. I just wanted to let anyone experiencing these issues know that we've address this and changed the way NextGEN and featured images work in future updates to alleviate most issues.
The main change will be that once you add a featured image from NextGEN, it will actually create a copy of that image in the normal Media library and use that for featured images.
This is a bit cumbersome, and it means that changes to an image made within NG would not relflect in featured images since those will now be display from the media library.
On the positive side, the fact that featured images are using the media library as expected means no problems at all across other themes/plugins that work with those images.
Wanted to let you know this is coming, and also see if anyone has feedback on that approach. Thanks,