The thing with the DT drum sound is that MP was in charge of the production for so long that he made sure his drums were up in front of the mix and had a very specific sound (same thing applies with guitars and JP), sometimes sacrficing other stuff because of it (keys and bass, mostly). When he left and John P became the main man when it comes to production and sound choices, the drummer perspective was no longer in the equation. Add this to the fact that MM joined a 25 year old already stablished band, so for a while he was just the new guy who had to go along with the previously existing band dynamics.
The drum sound on ADTOE wasn't bad at all, just mixed a bit too low (specially for some of the cymbals), but that would've been "fine" if we weren't coming from the MP-produced era. Then the self-titled came along and they decided they wanted to experiment even more... with the drums! Again, Mike, the new guy, had to stick with it; and even Rich Chycki had to do what the producer asked him to.
The Astonishing was even weirder in the sense that it was built entirely by John and Jordan and the other guys only had to come and record stuff and that's it, no involvement with the other aspects at all. Now, with DOT, A View and whatever comes next there's been a lot more involvement from MM and it definitely shows when it comes to his drum sound. Is it always to his liking? Not really, but that's the producer's choice/fault really. I don't think anything else will dastically change unless they put someone else in charge of the production.