Lack of discrete graphics, yeah, may be a problem
In order to play a certain kind of games, i.e. classic games ported to OS X using the popular SDL library, I depended on the dedicated GPU to render the game resolution correctly on my 15" Retina display. If accidentally (and that happens quite often) the integrated GPU was used for the game graphics because of failed automatic switching (something failing in SDL's hacky logic, I presume), the image would appear stretched and misplaced on the display. So while this issue is easily fixable on 15" MacBooks since you can use their discrete GPU, I don't know how 13" ones can cope with it, unless SDL team issues something about it
Small Retina MacBook Pro seemed like a non-starter for me, partly because of that, and also because of the insufficient 128GB disk space.