Rome total war. The only feature I enjoyed was the pre-combat speeches, which KICKED ASS. Everything else was light.. and buggy. Even easier strategic map than Medieval. Some fantastic looks, but it was a smaller game. Count the unit types, if you would, and please compare to Medieval. Was not suprised that M2TW continued the process.
Master of Orion 3. I liked the look, but it was extremely buggy. It isn't as bad as everyone would make you think, but it was only good enough to let you know how good it should have been. Of course, in retrospect, for a project with the lead developer fired a year before release, along with half the dev team, it was better than I should have given it odds of. As for those who had only played MoO 2, well, I can't imagine what they were thinking.
Civilization III. It was slow, laden with pointless ugly 3d tiles, and there were many features that were in SMAC that deserved the full treatment. There were many bad spinoffs that should have made it clear what was not worth pursuing. It also was the game that made me realize that the editors, (and perhaps writers) of Computer Gaming World were a bunch of @#$%.
Warcraft III. It's 3d. Sadly, it set the standard for RTS graphics for years. It was neat, but there was no filling.
Supreme Commander. I don't know why they decided to go with three generic factions, rather than two different ones. Blame Starcraft? Good MP, but I can't in good conscience consider it better than OTA or TA: Spring.