I do believe that the addition of the new reputation system will be good for the longevity of the game and I applaud your efforts. It will add a new form of advancement, both in gear and character, to the game that is sorely needed. In addition I do understand the Doff changes from an economic point of view and accept them for the most part. With that said though there will be several negative impacts on gameplay that may have been unintended from these changes that I would like you all to think about in your next meeting.
The players have become accustomed to the current STF system. And while it is true that you are adding new rewards for us to participate in the Omega reputation system it is also true that you are creating a barrier between us and the existing rewards. This is especially true for those of us who have not entirely finished a set be it weapons or an existing set. To remedy that I would suggest that you keep Prototype Drops in the game as a random chance at the end of an STF even if the odds need to be lowered. Only allow them to be used in the existing STF store for the existing Omega/Maco/HG sets and/or weapons not for any new stuff. We will still do the rep grind for the passives yet we won't be quite as unhappy while we are doing it.
The doff changes are understandable if a bit off the mark. You see, the big two problems that currently exist are very simple when the game is viewed as a whole instead of just from the Doff system point of view. First, dilithium is in short supply and high demand at every turn. That is not entirely a bad thing but I would suggest that instead of a recruitment pack costing Dilithium that instead it should cost about 50,000 energy credits. This adds a much needed EC sink to the game and helps to reduce the rage. The second problem is that we need to be able to 're-roll' doffs to get the right type for our starbase projects. That is the main reason I personally use the doff grinder and I'm sure many others are the same. To that end please create a new grinder that allows us to trade 2-3 doffs for one doff of the same quality but of a specific type. IE trade 2 white doffs for one white SECURITY doff.
And finally, new dilithium dailies are sorely needed and I hope that there is a way to gain alteast 4,000 a day from new dailies in the new sector block. I don't care how complex or detailed they are I"ll settle for 'kill 5 waves of tholian ships' just as long as there not breen.
Ignoring the dilithium costs for new doff packs Cryptic has basically created a standard framework for current and proposed groups which will carry forward and (hopefully) speed up additions of new similar content.
The STF's fall into the OMEGA force rep system and would have been anomalous to have been ignored. While the changes may not be liked by many it is plain to see why it has been done. I do hope however that the dilithium reward for the missions are kept as some straws can get very heavy and the rep sink is already effectively reducing there outputs.