I am preparing for MoP and in the course of finishing Cata I xferred a couple toons to another server but continued to run heroics for valor and occasional FL runs. Once 5.0 comes out I'll need to re-evaluate whether I need to transfer the rest. So far, conceptually the downsides seem to be:

Cannot trade, so professions across toons would be nerfed (ie can't enchant an x-realm toon's armor, etc).
Inability to collect the same guild rep or contribute to the same guild's xp for the x2 or x1 server
Complexity in ensuring that the right toon loots the right thing (for example the tailor needs to be the one to loot the cloth).

Anything I am missing?