The planets would be impregnable... Even without custom star-bases, multiple star-bases, and multiple other defenses, would quickly change the game dynamic so that fleets would need to be ridiculous in size, and people would play more on the defensive than anything else. This would probably give research races a ridiculous advantage, too.
I guess I should first state that I am a single player 100% kinda guy, have never played a game of Moo2 online, and the only MP I ever did was a hot-seat game that did me in for MP forever.
I think that your right, planets would be far harder to conquer (which is what I'm after obviously), but what I am after would be the ability to build up planetary defenses so that no enemy could just build his 'juggernaut syndrome' fleet and easily roll up all other empires, one after another, rapidly and without fear of losses slowing him down. If a planetary defense could wipe out small to medium sized fleets, then there would be no quick grabbing of well defended planets, and you would have to try to pick off worlds that were not as well defended. Keep in mind that just because you could build vast amounts of defenders doesn't mean you could afford to build them everywhere. Basically, the more you build on one planet the less you can afford to build on all the others.
I realise that several other issues would have to be addressed as well, not the least of which would be the command point issues, the lack of limiting maint costs (In late games, I always end up with all the cash I could ever use, so there wouldn't currently be any reasonable limit on planetary defenses from a financial point of view), as well as needing the planet to be able to support the defensive works locally (In essence, new planets could not build large defenses because they would lack the support infrastructure, and building and maintaining this should be far to costly for a just settled world to be able to do).
In this manner, newly settled worlds would have to make do with much lesser defenses, would represent a drain on the imperial economy (rather than a bunch of pop 1 worlds with spaceports and set to build nothing but trade goods), and this would make the weaker worlds more attractive for a conqueror to try and take to gain access deeper into enemy territory, and allows a long settled, well developed world with correspondingly stronger defenses to continue under your control until such time as an enemy is willing to pay the cost for taking it.
In terms of gameplay, this would, IMHO, go a long way towards fixing some badly done elements of this incredible game, and would actually make for that long elusive 5th X (eXperience).