I am amazed at the speed, I have been so used to disappointment with online amiga gaming and now this WIP comes out and kick arse! Having the developer around to help with problems has of course been fantastic too. 
Just some thoughts, I know you are planning on some if not all these things, but I just wanted to put it out there just in case.
Wish list:
Chat function
Better quit function
GUI in general, but also for network stuff.
Checks for the 2 different file type names for 360 controllers.(Mine is fine now, but others will have this problem.)
Taunt button.(So I can taunt Horace and FOL with one key press mid-game) 
Of course that will have to wait until you are finished with the main work, which is excellent so far.
Version 0.9.13beta11 has many of the features you requested
http://fengestad.no/wp/fs-uae/download-beta* Can specify joystick port mode (useful for forcing CD32 gamepad emulation on non-CD32 model).
* Overlay GUI "console" displaying chat and emulation warning messages.
* Emulation will now also close when using the quit function, even if the emulation thread is non-responsive.
* FS-UAE continues in offline mode if net play connection is broken.
* FS-UAE continues in offline mode if a desync or other net play error occurs.
* On-screen connection dialog showing when connecting to net play server.
* FS-UAE will keep try connecting until successful or manually aborted by user (net play server can be started after clients are started..)
* On-screen dialog while waiting for net play game to start (waiting for other players...).
* Integrated text chat for net play.
* Net play HUD / status bar can be toggled on/off with the TAB key.
* Support passwords for net play games (option netplay_password).
* Fadeout effect when closing the emulator.
* Some name changes in custom / advanced input mapping.
* Added aliases for Xbox 360 controllers with slightly different names on some Windows systems.
For net play. this version requires that you also update to the latest net play server.