Presumably you'll have multi-protocol clients developed that can support the various flavours and blockchains that exist.  So in that case a merchant who takes the time to incorporate btc into his site will just incorporate all the different flavours in one go at no extra cost.

IMHO the key is volatility.  Since transaction fees are all negligible and if we assume all the different versions are equally secure, the only thing a merchant would care about is the volatility of the different versions.  You're always going to want the one that is least likely to fluctuate w.r.t your outgoings.  e.g. if you are reselling cars that you bought with USD, you want to receive whatever will fluctuate least against USD.