Some criticism so far:
Class icons next to the class headers and maybe in the player list would make things a little more aesthetically pleasing, they would also help show what class a captain is playing.
Something that would be very cool is a way to view pug stats of someone including class percentages, DPM, K/D/A etc. Right now the player list doesn't seem to do much. If you ever implement steam authing, direct links to peoples ESEA/UGC/Steam profiles from the player list would be awesome.
The AFK timer should only activate before captains begin picking, it seems to go off too much for me.
I get this message
Lost connection to the TF2Pug.me server
The server may be down or you may have lost connection to the internet
wayy too much, and there's no way to X out of it without disconnecting and rejoining. Disconnecting during picking phase will lock you out and you won't be able to rejoin with the same nick.
A minor issue, I saw some people flooding chat. Maybe use a less restrictive slow mode similar to twitch.
Some people have nicks longer than 10 char, I'd like to see it increased to 15.
The help button doesn't seem to do anything for me.
The sidebars are a perfect place to put the server status, how long ago a game was started, etc. There are free server banner websites like this:
http://cache.www.gametracker.com/server_info/192.223.30.242:27016/banner_560x95.png?random=38630
but they're pretty ugly and don't go with the minimal theme.
I realize the mumble connect icon is pretty obvious, but unfortunately it seems it's not obvious enough for some people. Maybe have a green arrow pointing to it after someone is picked that says "click to connect to mumble" or something. A server join button would also be nice instead of having to paste the connect info in.
TF2Center has that nice mini-tutorial when you first open it that prevents a lot of confusion.
As some people have already said, the config could use some tweaking and I'd like to be able to play with hats. Some servers I've seen have AFK timers in-game which are pretty neat and help with the "r u guys rdy?!!?" problem pugs seem to have.
Not sure if this is already in, but a way to vote for the map either on the website or in-game is needed.
I personally like to see the (captain) has picked (player) on (class) messages in chat.
I like the captain only system in favor of an alternating automatic pick system.
All in all it's good. Keep up the good work =)