I like this idea because it allows you to essentially create terrain on the map, something that is very tricky in a space game.

It already does if you research the tech to do so

The problem is that a percentage reduction is not enough. Player-built transports have movement rates of 20+ so even with the -50% reduction you can still fly through the defenses. I'd rather have the rule that you can't invade a planet until you have killed the starbases protecting it. Or, if you want to do it with speed reductions then make it cap the speed to a flat max 2 hexes/turn. That would make the transports vulnerable to counterattacks and force me to take out the starbases first.