Well considering you're making a superior prequel out of the inferior sequel, I'd say take out a lot of the fluff and crap that 12sky 2 has. I'd vote for the lack of 150%, warlord rares/elites/cape, absolutely nothing past m33, just making m33 as hard as it was in 12sky1 is plenty.
On the other hand, I'd say trading cp would be nice, MAYBE the war brackets but definitely the old yang map. Three factions is plenty, it's less fun with nangin imo. Just the four capes is also plenty (three rare, one elite) too, no need for capes at ever level, or the ability to enchant rings, neckies or capes.
Finally, I'd say put SOME item mall items into ingame stores, but keep others in an actual item mall that people have to pay for. I'd suggest you make it all really cheap and of course, all money is in the form of a donation and goes to the funding and maintenance of the servers.