Here are some suggestions that I thought up (many may be from OG Jailbreak)
/redie I think this is important because it keeps dead players engaged (servers that don't have this can get very boring very fast)
As Worgee said, gangs
Maybe not too elaborate of a shop system, because it can cause problems (as seen with our last JB server)
Keep events + event coordinators
Keep old admins (for the most part) and also add new ones (more admins are needed because of this new influx of hackers from the FreeToPlay update)
A more defined rank system, the last ranking system from old JB was confusing (I never understood how you got points) maybe have a ranking system that tracks CT kills, successful days as CT/warden, etc.
Basically all old plugins as JGuary said, !o, !w, !voteday, !vg, !rtv, etc.
Make it so ts can talk to CTs 30 seconds after round starts (like old server) and dead can talk to alive
Also I didn't really understand the !deputy command, didn't really see its purpose