Hm, let's see. Limited to prog bands with keyboards:
A classic prog metal band should cover The Killing Hand. Maybe Circus Maximus, considering how they cribbed half of DT's discography for the riffs on their first two albums
Haken should cover Under A Glass Moon, Scarred or Voices.
Symphony X should cover The Mirror. The Glass Prison would also be really interesting from them.
Leprous could cover Surrounded, but make it weird.
Riverside could do a cute live mashup of JLMB and LITS, but I don't know what studio cover I'd like to hear from them. They could do a cool Home.
Let's put Seventh Wonder on LSOAD duty.
And finally, OSI should cover Lie
As for metal and rock bands, I really don't know many that cite DT as an influence that I would actually like to hear covering their songs. Sonata Arctica could cover Another Day or Take Away My Pain because it's my other favorite band and I know for a fact at least one guy in the current lineup loves Dream Theater. Otherwise my minds is drawing a blank.