Asking if they will fix the queues is kind of like asking "Should I get this gangrene looked at?"
They are horrible as they are. The developers must be aware of this because it is impossible not to see. I have confidence they will be fixed. I don't know when. I haven't seen it listed in the engineering reports.
They have to do something though. I have never seen a game with a worse pvp-matching system.
The suggestions in the op are a good list of solid improvements that should be seriously looked at by the development team... except the additional chat channels aren't really necessary if it auto-teams each side.
I'm not sure the numbers imbalance will get fixed. Making it so that the match won't begin until the teams are full just won't work; you may end up stuck there for half an hour waiting for people to zone in; which is even less fun than uneven teams.
The only way to fix it would be to make it impossible to queue for more than one arena at a time; this is what is the main cause the problem (get 5 people on each side queuing for the same 3 arenas and they will all launch at once, but there is nothing to say that all the players will go into the same one). However, this would greatly increase the time spent in queues, since you have to wait for a specific game to launch rather than just go with whichever pops first; so I don't see Cryptic doing it.
that thread certainly does give the appearance that Cryptic was previously unaware of any queue problems, and that future fixes (if any) will be many weeks away because they must first carefully collate, present and evaluate this new information before they can even think about making plans to develop, test and release any kind of fix.