When Trunk says the DT song sounds like DT, I fail to see how that could possibly be an insult. The guy likes DT, and in light of the changes that have occurred, the fact that they still like the same band is important!
The part about MP still being the best was probably the reason he took the tweet down, but I don't even understand how someone could think that the first part was an insult.
I think it's a little more passive aggressive than that. If someone asked you what you thought of the new episode of Doctor Who, and you went "well... it's definitely an episode of Doctor Who." See what I mean? Not exactly tumbling over yourself with the superlatives, there.
And even less so if you were to add "Would've been better with the old guy writing."
For what it's worth, though, I didn't think Trunk was belittling the track, either. Not intentionally - he's playing it on his radio show, for starters, so he's clearly not cheesed off by it. He was never going to start going "oh wow this is SO MUCH BETTER than the last few singles," though - to raise the paddle ominously above the corpse of the girlfriend metaphor once more, you wouldn't start spouting off about how your mate's ex is "way better off with her new man!" while your mate's in the room. And chances are you'd be a little cold to the new guy simply by virtue of him being the new guy, so you know; fair enough.
I do consider it a snifter churlish for Mike to go "look - see? should've been me!" but it's not some massive faux pas - not a million miles away from putting your reviews on a poster, I'd argue. I'd advise Mike to let it go, though. It's a brave new era for a band who was, with their last album, threatening to become a little stale, and for a musician who spent the last couple of years going on about how he probably wouldn't use JLB if he were starting Dream Theater now and how he could've ended up as a metal drummer and isn't just about the prog no-sir-ee.