I think a full rework is a bad idea. We should trying fixing what we have.

Current Major Issues:

Job Balance- This will always be an issue in both PvE and PvP and you can only fine tune as patches go on
Easy Rank Up/ No Demotion -A lucky player can be carried into a new tier more easily than in Feast with no chance of demotion
Crowd Control- We have a lot of CC with little ability to deal with it. Temp immunity may be the solution here.
Counterplay- This sort of goes hand in hand with CC, but also there are things like dealing with the SAM LB when you have Bahamut or Bishop out. Maybe it should only work with direct attacks.
Cheating- We all know it does happen, but SE has never addressed this in PvP

The Minor Issues:

Chat Spam
AFKing