To my knowledge there shouldn't be any difference, at least theoretically.I haven't had a chance to play with SwitchOS yet is there any performance change if you use it and aren't using any of the L2/L3 routing features?
In the past, there was a difference in feature set, I believe LACP bonding was added first to SwitchOS (I may be mistaking here)
However, RouterOS is updated MUCH more frequently, and it seems that new (even switching features like 802.1x, that was added in RouterOS 6.45) is added to RouterOS first nowadays. From my perspective RouterOS is the better choice, now if they would just start shipping devices with a more secure default configuration I would be happy.... there is so much stuff you need to disable.