[Suicide Junkie]

Homeworlds will grab a spaceport ability, a resupply ability, a SY ability, and the various resource abilities.

If you want it to look nicer than having two spaceports, what you can do is have some "Legacy City" type facilities, which do everything, but are so expensive that they can't be built while the game is going.

That way, you get a SY, and lots of Cities on the homeworld... everywhere else you will be building from scratch, so it should be fine.