I guess maybe if MLB were to find a way to review all plays in near real time, the challenges wouldn't even be necessary. Maybe they can use AI examining all the video angles on close plays to get a determination in seconds, then relay to the umps if there's a change. I agree adding or subtracting base runners isn't ideal, but if challenges are only made on clear cut bad calls then it should really also be irrelevant. Also, it shouldn't affect the rest of the sport since most leagues don't have the replay capability. Dunno, just thinking about it off the top of my head. Counting it as a mound visit probably isn't punishing at all in 90% of the cases.
If you really want to mix things up, you could make it that if you challenge and fail, the other team can make one of your players not in the game ineligible to enter. Obviously I doubt anyone would ever vote for that change, but not facing that elite closer sitting in the bullpen as punishment would spice things up a bit. There'd also be a bunch of ticked off closers.
More realistically, maybe the manager gets tossed if they unsuccessfully challenge.