That way the player has to prioritize defense around planets.  I like the idea of important locations having the best defenses, like Earth and Reach in Halo.  But in Sins by midway through the game you can max out tactical slots at every planet making every one of them the "best defended" and it takes away from the idea stated earlier. 

This would also hopefully slow down expansion because some astaroids may not be worth colonizing if you can't protect them.  In a typical game every single habitable world gets colonized fairly early.  This limits the need for patrol/scout ships watching unoccupied space.  I like the idea of small scale boarder skirmishes, and you can't have them if everything is colonized.

You can't directly give them upkeep by a percentage, but you could make them generate a negative amount of credits and resources through a passive ability.

And btw, the ships themself don't have any upkeep, but the upkeep lies in that your income gets reduced by a certain percentage when you have completed the research.