No opening of new tabs (middle-clicking)
You mean in the WebGL app, or on the website? It should still work on the website. In the WebGL app it's true that doesn't work, but it didn't in Flash either :)
Long loading time to start up
Yes, this greatly annoys me too. You can minimze it by installing FireFox nightly, on my PC I can get it down to about 4-5 seconds. I'm working on some stuff to make it even better than that.
mods are fully limited to only members
The important thing to understand about mods are that they run on the server. For this reason, a game with mods takes about 100x more resources for the server to process.
quickmatch only works on 30 templates instead of having a rating for whatever template you want to play on
Once you get to 40 wins, you can add your own template.
Can't see other player's banked boot time
Hover over the clock in the top right corner.