I could accept transporter usage for non-organic material, so no beaming of people. Agree on no holograms and no cloaks (it was unknown technology in TOS). I don't mind the protein resequencer, it would be a way of recycling materials into something useful whilst on the move. No photonic torpedoes.
Definately no TCW or Xindi. Adjust the Suliban to experiment with genetic engineering on their own (no future interference), as it was something that could have been looked at in more depth. Have the Romulans pulling a few strings, so long as they aren't seen on screen--ships and disembodied voices only.
Keep Malcolm as Armoury Officer, but introduce a separate Security Chief/MACO Commander. Keep T'Pol as Science Officer, but with a more appropriate Vulcan look (black hair and no catsuit). Either give Travis more to say and do or have the role as just a recurring one. A first contact/diplomatic officer would be a sensible addition, they could act as a mentor to Hoshi. Make Archer a decent leader, also make him something other than American (New Zealander perhaps?). Drop Porthos. Keep Trip/T'Pol.
Absolutely no Ferengi, Borg or Klingons. Romulans are only ever in the shadows. More Federation species (I wanted to see the Deltans make an appearance). Drop the Orion female twist.