I prefer clusters.

It leads, in my opinion, to interesting situations which are not possible in a scatterd game.
For example, on my actual game (large), there is one cluster on the bottom with NO major civ in it at the beginning. Between that cluster and the rest are about 6 sectors of empty space. So the first civ able to send a colonyship over that distance will get the planets down the: A much longer colonization phase, everyone trying to bridge that gap with space stations and range+.
It's a matter of taste, but I prefer that kind of challenge to a map where every sector is of equal importance.