I think Transatlantic would be the most popular answer, or rather, anything with Neal Morse. I loved that Mike was able to play on the Testimony Tour with him, and I love the live DVD with his performance! Great stuff. I wouldn't mind seeing Mike playing more of Neal's solo stuff live, no offense to Collin because he's an amazing drummer in his own right!
If not Transatlantic or Neal Morse solo stuff, I do think Mike should get up with Paul Gilbert again and form another covers band/project... maybe do a full-blown tour and do more than a handful of shows on the coasts. What could they do? Well, I wouldn't mind seeing a tour of what Mike considers his favorite songs/songs to play and cover, showing a wide-range of styles and genres that Paul Gilbert would undoubtedly be able to cover (cuz let's face it, the man can play anything). Maybe something that's like a Chronological Journey of his favorite songs growing up to songs he loves today. "Portnoy's Choice" Tour or something, ya know?
If not a tour, I wouldn't mind seeing Mike cover a classic album in the studio with some great guest musicians, since he likely has one or two classic albums he wouldn't be able to cover with DT now, it wouldn't be so bad if he decided to record them and release them as studio recordings. I know I'd buy it, especially if it was Rush, Yes, or Genesis. Part of me REALLY wants to hear him cover Rush's Caress Of Steel album, mostly because I'd love to hear SOMEONE cover "The Fountain Of Lamneth" and I would love to hear Mike play "Didacts And Narpets"! I think a bit of rearranging on TFOL could make the piece more cohesive and full and less a suite of songs strung end-to-end. Also, it'd be fun to hear him cover "I Think I'm Going Bald".
-Marc.