Either way, realnowhereman is on point saying that this will most likely be solved way before it is actually an issue. The fact that there has been so much talk about this is a very good sign in itself. In fact it's very likely that a new system will begin forming during the 25 BTC reward block era, which is when tx fees quit being negligible amounts of the total reward. They will still be a small percentage (even after the 25 -> 12,5 drop, which is why I said this is really only a problem next decade).
This is speculation based on current tx amounts though, if Bitcoin usage significantly increases tx fees will be a bigger part of the picture sooner than we think. It won't accelerate the problem though because that is solely related to the amount of fixed reward. The reason for this is that increasing usage will also raise the price of BTC thus leading to more mining investments and thus a stronger network.
These and probably a few other schemes might give us a proof-of-merit model that rewards honest mining pools. Possibly with extra Bitcoin from the destroyed fees or maybe decreased difficulty. I'm trying to salvage any ideas from the prook-of-stake model that might serve to add a level of trust to a pool that it will include transactions and be amply rewarded for doing so. It would be a nice bonus if it could mitigate the risk of an unknown 51% attack.