I've been waging a similar battle. Although I am currently making money @ $50NL, many times the table selection and win-rate seems MUCH better @ $25NL. At first, I stuck with $50NL, but one night there seemed to be NO good tables and I was sitting by myself trying to start tables and no one would join, so I fired up some $25NL ones. DeucesCracked coach WiltOnTilt has said in one of his videos that you shouldn't think of yourself as a $100NL or $50NL player or whatever stake you're @ and that you should probably play across 2 or 3 stakes. So, then I decided I would just pick the best games of what was available across both stakes. That did work well, but then I noticed that the juicier games were often weighted to $25NL and I was starting to log more hands @ $25NL and it just felt like I wasn't tackling $50NL head on and that I should focus on it for the same reasons Micro mentioned. I feel like if I don't put in enough quality hands @ $50NL that I am hurting or at least delaying my chances to improve there and beyond. So, for the time being I'm only looking for $50NL tables unless the selection is so dire I might do some $25NL ones. But, who knows, it's possible I could change my mind again and do both.

I don't think there's an easy answer because you have to balance out the best games versus how profitable you can play at one stake versus another versus what you are learning or not learning and the problem is compounded because the games are so dynamic that it's difficult to root yourself on solid ground in terms of consistent behavior or results.