Each move has its pros and cons. I prefer roost unless you plan to pass a wish to another Pokemon, which I personally wouldn't use Togekiss for. Roost recovers the same amount of HP in half the time. And if you don't run protect, Togekiss might just faint in the turn that wish takes to take effect.
Roost has its cons as well, though. You lose flying type for the remainder of the turn, so a grass/bug move will do neutral damage. Then again, if you have no speed investment on Togekiss then this doesn't really matter.
Hope I helped!