TMOLS is a top 10 song for me. Two of JPs 10 best solos, and the third-best outro, behind TBOT and Octavarium.
The instrumental section works fine for me, but I do think it could've been cut down. If they just did fast riffing for a bit and then cut straight to JPs solo, then the unison, then the breakdown, it would be an even better song. The biggest offender in the section, IMO, is those two Rudess leads on the organ-ish type sound. It's that classic Rudess "What if I threw something weird in here?" vibe that doesn't really go with what everyone else is playing. In general, I'm also not a fan of the extended instrumental riff sections--unless they're amazing riffs, you might as well get to the solos.
Even though there are some moments that drag or annoy, though, the song's highs erase them from my memory as I listen.