MPE is an enhanced civ2 FW with multiplayer option, a more aggressive AI and some minor changes (like more eventsspace for scenarios).
ToT has also multiplayer support, the same (?) AI but also some really new features as multimaps (you can play one game on different maps=worlds), it comes with the original game (like civ2), an enhancenced original game (you can continue on Alpha Centauri), a Fantasy and a SciFi game.
ToT has in my eyes also the ugliest terrain and background graphics of all civ games (but you can look for some replacements on the net)
ToT has much better scenario options (more eventsspace, new events values etc...), but unfortunately not the scn editors known from FW
------------------
Civ2000