Really, and its a terrible reason to write an entirely other app, but I just don't like the styling on the tabs :/ That tabbed Windows GUI is just so damn ugly it actually distracts me.

While I generally like ConEmu, I personally find the multi-line selection to be pretty poor compared to something like iTerm2. (The way the selection buffer stays at the same coordinates while the text underneath it scrolls up isn't all that awesome either.)

ConEmu's performance for TUI apps like vim or weechat+ssh is not great.

Not a factor if you don't use those sorts of applications, but a bit of a deal breaker if you do.