Puppet system would probably mean major changes to the game. Light-weight variants on the level of "planet spawns a new minor civ that immediately makes an alliance treaty with you" might be possible, though.
One thing that I'd like to add to attacking planets is the possibility of orbital bombardment by ships. Not as an abstract invasion tactic choice but an actual strike with ships targeting planetary buildings and population. Keep the "only transports can conquer a planet" rule, which is good, but ships could add to the invasion by first "softening up" the resistance by blowing up buildings and bombing the population (with the additional risk of the planetary defenses shooting down your ships).
Besides, "it's the only way to be sure." 
