No game in the genre has approached the awesomeness of Master of Magic or the first Master of Orion (not that MOM 2 was a bad game mind).
Unfathomably complex is not what those games were. Deep, involving, emergent and atmospheric yes, but not brain burningly obtuse. All these indie games just don't seem to get it, but good luck for trying and you keep getting my money anyway as I try to scratch that unscratchable itch (Well, until I get the old 486 dos machine out of storage again).
Hoping the UFO:Ememy Unknown remake turns out good. The Pirates! Remake Firaxis made almost nailed it, and in some way was superiour to the original. If they get XCOM right I'll start a kickstarter for them to get the rights to those other two great Microprose TBS games.