Well, I'm sure people get tired of my posts beginning with "what my league does..." when presented with this question
But the RB value/scarcity issue comes up so much, I offer this advice to anyone looking for ideas. Also, our league is a one keeper with the flex as well, so I think I know where you're coming from.
My league adds QB as an option in the flex. Not all providers support this, so you'd have to check with your scoring provider and see if it is an option. But because a 2nd QB generally will score more than a 3rd RB in most scoring systems, this adds a good deal of value to QBs. At the same time, it doesn't add all the issues that most 2QB leagues have. Basically, if you have a 2nd QB to start, that's what you want to do...if you don't you can start a RB, and if you're really desperate you can start a WR or TE.
I have found this really evens things out and gives owners a lot more options dealing with injuries and such. I led my league in scoring last year juggling Westy, Chester Taylor, and McGahee (my keeper)...all good backs but not LT or LJ. It is because I had Peyton Manning and stole Vick several rounds deep into the draft, and of course he blew up. Those two starting almost every week (Vick in the flex) made up for my deficiency at RB. It does undermine the value of WRs even more, but that is not as bad as seeing 25 straight RBs taken in a draft.