They don't like other Art Collectors in their alliances. Similarly multiple EBs won't work well together unless 1 subjugates his scoring position to the other. Well, Berserkers can hit the same worlds in tandem and each gets full points for the kills made. It's called the cooperative kill. So if 3 berserkers come to a world and 1 drops a PBB while the other 2 do AP the first berserker gets the 200 point bonus and points for the kills and the other two get full points for the kills.
Pirates often work well together since they score so poorly in general.
It is not uncommon to have 2 in an alliance and neither wants to plunder. They both will want a good fight and it's good to get them on different fronts so they don't inhibit their capture abilities. Multiple merchants - they work well together also since they have such a huge scoring advantage. In fact having more than 1 merchant may be a peaceful way to stop a merchant from running away with the game. So an alliance of 5-6 could house 2 merchants.