I think that it sounds like a huge advantage on paper, but I'm not convinced that it's really an issue in actual play (though I'm not denying you may be correct). I have to imagine that all but the most rigorous, mind-like-a-trap player is going to experience enough "analysis paralysis" given 100 spells per level that they'll just end up using a few tried-and-true additions to their typical assortment.
And heck, if the player is going to go to all the trouble to examine the SpC six ways from Sunday and find the cool bits, I'm not going to deny him the benefits of his effort.
In my Monday game, our paladin has been using spells from the SpC quite a bit, with no restrictions as to whether he access to them or not. We've also glommed onto
lesser vigor being a superior out-of-combat healing spell. In all, it's been pretty much what I mention in the first paragraph; an addition here and there. I simply have not seen it be a problem.