There have been many bug fixes and small improvements to the existing clan features. The bug with exiting a game when spectating is fixed. Also, clicking HELP during the tutorial now works. That has been broken since at least 2.5.
VW3 will work with all existing accounts. The beta will only work with vortexwars.com accounts since Kongregate and Armor Game accounts can only be used on their websites. Sorry about the inconvenience.
It would be possible to allow signing in with a vortexwars.com account on Kongregate or Armor games, and Kongregate and Armor Game accounts to add a password so they can sign in on the website. I need to do some experimentation with PlayerIO's authentication api, but adding a password might require moving accounts out of PlayerIO, which would be a lot of work and isn't a high priority right now.