I agree with this generally. My view:
The ships should be automatically fleeted and in guard mode near the shipyard that produced them. Problem is, if you try to put them in orbit, you will likely find at least one situation in which the orbit is already full, so more complications ensue. Of course it is possible, though unlikely, that fleeting them overreaches the current logistics. Then just do as game does now when ships meet in the same hex, fleet as much as possible.
I wonder if Colonies should have a Rally Point button, like shipyards. The default would be the same as current. But one could redirect in many situations (fleet in transit, change rally point so that when fleet arrives they go on to whatever. No need to find the fleet on an immense map. And escort ships or the 3 defense ships could also automagically be redirected. Planets would then be more attractive as destinations from other points.
Personally I think these 3 ships per colony is a little OP, and at the same time (self contradicting, I suppose) the ships I have gotten aren't that useful to my current plan, either defense or offense. Perhaps when receiving this perk, the player gets a dialog with a choice of ships. (All with poor speed, because they are supposed to be defensive.) I would prefer all beam ships as of Beta 4.
But it's a good thing to bring up.