I don't see how it would be all that time consuming to have the player choose a colony capital location as their first act when they enter the colony screen after colonization. When you first colonize a planet, you are taken to the planet screen anyway so you can start placing your structures. The capital would just be the first structure you placed. This would allow for optimal capital placement both for players who prefer isolated capitals or who prefer capitals with maximum adjacencies. As for the AI...well that's where the debate about isolated capitals vs adjacent capitals becomes more relevant, because there would have to be a decision made on how to bias capital placement for those empires.
and i think this debate wouldent actually be all that hard to solve
as long as the capital stays at +1 adjacency its subpar since adjacency bonus's are not used by the capital the fact that its +1 to all adjacencys is nice but not enough to overcome the fact that they are not returned
at +2 adjacency bonus it become even for any basic building bonus ( +2 one way = +1 both ways) again the plus to all is nice but surrounding it with different types of building now wastes the adjacencies those buildings create
at +3 it actually becomes useful to place buildings next to it
so to paraphrase this
keeping the adjacency bonus as is = isolate the capital
+2 indifferent to position
+3 put it as central as can be