I know I'm late to the party in regards to commenting on the Reputation system, but since it seems like Devs actively read the forum, I though I'd add my two cents.
I think there is nothing inherently wrong with the concept of a Rep system, and the idea is a fine one, but as it stands now it feels like nothing other than mindless busy work. It's true that there can be a simple joy in filling up a progress bar and yielding slow and steady progression towards a goal, but the addition of multiple commodoties needed for each project makes the whole thing feel like an irritating and boring job rather than a game. I assume they were added to give a useful function for underused items that were accumulating in people's banks, and/or to provide a light EC sink, but the end result is just tedious.
If reputation projects could be finished with just Omega/Romulan marks I think much of the feeling of 'grind' would be removed. There's fun to be had by playing the missions (STF or Romulan), gaining marks, then filling up progress bars with those marks heading towards an unlocking goal. Things become cluttered and begin to feel like work once you add in the need to replicate endless additional items or run around to various star systems to collect them in huge quantities at the best prices.
Noone really wants to feel like they're playing a second job, and I think this is a simple change that helps to remove some of that grind feeling.