Unfortunately, at any scale other than the smallest map sizes, this currently doesn't seem possible with most races. I've been trying to play a proper 'Galactic Domination' game where the only victory condition is controlling the majority of systems.
Beyond that, it's all about pumping out happiness infrastructure to counteract the penalty, but even that fails after a certain point. However, this is really only relevant in the early game. There are two techs which collectively bump the penalty up by (I think) 4 planets.
This is my biggest frustration with the game at the moment as well.
