I agree the development of a countermove would make him even more unguardable, but the biggest reason the Bucks get in trouble is that that other teams go on runs and get momentum when they sit Giannis for rest.
Music has pointed this out in the game threads, but when Giannis sits Bud routes the offense through Middleton which often results in turnovers or bad shots that end up in fast break points or wide open 3s on the other end. The pattern is that Giannis is in during the third quarter and part of the 4th, they build a double digit lead and by the time he's back in it's down to 3-5 points and the other team is in a rhythm.
The problem with Middleton's game is that on offense he is a poor man's Carmelo Anthony. When they route it through Middleton, the offense goes stagnant and it gets everyone else out of rhythm. Middleton's also not good enough or athletic enough to beat elite defenders in isolations which leads to turnovers and contested shots. When Giannis is in, even Middleton's occassional isolations look better because the Kawhi Leonard/Al Horford elite defensive players get matched up with Giannis which allows Middleton to attack lesser guys and he's much more effective.
If they go iso with Bledsoe, things tend to go better because he is a great slasher and he gets the defense moving and keeps everyone involved.
The challenge will be how to manage those minutes when Giannis sits. Bud's keeping his minutes in the 32-34 range most games. Not getting blown out in those other 14-16 minutes is what will be the difference in a successful playoff run (at least the EC Finals) and a second round exit.
Last night, the Bucks were -4 in 14 non-Giannis minutes. In Utah, they were -23 in 16 minutes.