Lessee...Alpha Protocol. Everyone here knows about that.
Star Wars Rebellion, I liked the game a tonne and played it quite a bit, but for some reason no one else seems to. Maybe it was too confusing for some, but the manual was very well written and explained everything (probably a cause for general dislike). Particularly for the Empire, hunting down the Rebel HQ entailled a very methodical and persistent intelligence gathering operation of sending probes, recon teams to every planet in the Outer Rim, heh.
Hmm...then again, I guess I see why no one else liked it.
Also : The Guild 2, people hate the micro, but eh, I rather enjoyed setting up every little bit of a system then watching it click.