I've seen quite a few posters saying that they are worried that the dragons will become like Skyrim's version of the Oblivion Gates where they keep appearing frequently, become repetitive and also spoil the ambient wilderness. However Todd said in the GT demo that from the 'inital get-go' dragons won't be present (or they'll at least be rare encounters).

So, by the sounds of it, if you don't want dragons - don't start the MQ! (And if you don't want them all the time, don't advance it too much)