In the last Ask Cryptic, I saw a lot of reference to new reputation systems for all kind of things. I'm not completely against it, but right now I just couldn't follow with all my characters. I'm part of a small fleet, so we still have a lot to do for the base. We don't even think about the embassy. I have not played my Klingon characters in months. I have difficulty keeping the pace of the reputation with Omega and Romulan for my 3 Federation characters. So adding more? I'm not sure. And I certainly hope that if you add a reputation system for crafting I will not have to start from scratch like I have to for the Omega, even after countless STF done before season 7. My 3 Federation characters have reached the top of crafting already, I would not like to have to do it all again.
So, I have nothing against the principle, but some adjustments will need to be made if you want it to work and keep the player happy. I have a lifetime, paid full price, I would not like to see the game crash.
On a positive note, I like the add-on bonuses for the reputation tier of Omega and Romulan. It add a bit more customization to the character. As I said, the idea is not all bad. But make it part of the storyline for new characters and give at least a head start to the veterans.