The one big minus I see, is that this makes it much harder to skip a system and build up to take next system(as before you could use a mobile builder to build up some turrets and a stardock and use those to build the force you take the system, just using the transport for the guarding force, now you have to take out at least the command center, and have enough forces left/send another wave(and protect at least one colony ship) before you can build anything in the system. I'd almost suggest a supply range of 2 for this reason.
Having it be more difficult to go deeper into enemy territory is a sensible thing, I think. This is pretty much inline with most other RTS games, and it increases the interest of the decision space, I think. With some starships and transports, you can still take those planets pretty easily. Remember: planets that are that far away are also not under AI Alert, so they are also vastly softer targets. So your forces are going to be a bit weaker going in (no turrets or immediate resupply or repairs), but the AI is also weaker because you are catching them off guard.
The only other minus I see is it makes mobile repair centers a bit less worth it, since all they do now is repair things quicker, which is pretty darned expensive for much of the game at 2k knowledge. Before being able to have them travel with the army was a nice perk that made them more valuable. Perhaps the repair centers need a slight boost (perhaps in their repair range?--its sometimes a pain to get a large swarm repaired, since you can repeatedly tell the units to move to the repair center and make them all stack and get repaired at once, but this feels rather exploity).
Mobile repair stations also have the advantage of being able to yank ships out of battle. You'll take many fewer casualties with a mobile repair station compared to engineers, depending on how constant the fighting is.
Edit: I think the best fix will be more things that are worth capturing and holding(currently all we have are advanced factories).
Yes, that is to be a major focus of the expansion. The supply changes are more about force projection and adding strategic importance to planet positions.
