I have two complaints on my WMC setup. The first is how tuners are handled with ad hoc recording. Say a tuner is on a particular channel, and I decide I want to record; it will begin recording from that moment! What about everything that is in the rewindable buffer? I want that too! Same with changing channels to one of the other tuners. I should be able to capture back a half hour if the tuner has been on that channel already. I think tivo does this with their tuners.
The second thing is stability. Every time my pc wakes, the resolution is wrong and I have to restart WMC. I realized this might be an EDID issue that is solvable, but it's been annoying to deal with so far. Also, after a restart, either tuners aren't immediately recognized, or some channels act like they are unavailable. This eventually fixes itself, but it's still annoying.
As an aside, I just purchased a newly released harmony touch in an attempt to consolidate all 15 of my remotes. Something really annoying is the slight delay when issuing commands. You would think such a minor delay would be negligible, but man does it add up when scrolling through the tv guide or other options. There's nothing more annoying then clicking up 6-7 times to get to the menu option, only to watch the selection overshoot by 2 or 3 because of the delay. Also, having no ability to control the mouse is a deal breaker. Maybe when the system is rock solid, there will be no need for a mouse, but my setup is just not there yet.
It's been really tough to solve these subtle problems, and that has be looking at the green grass over there on the tivo side.