Okay, first off I want to make it clear that I like the Reputation system. I even like most of what's been done with this particular Reputation track. That said it isn't perfect. These are just a few ideas I had on how I think it could be made better. Your opinion may or may not match mine. Now to the meat of this post.
The first suggestion I have is also one of the biggest - to reopen the STF store on DS9 and move all the Mk X equipment there.
○ The Mk X Anti-Borg Ground Weapons should be available at the ground vendor and purchasable for a combination of Omega Marks and Dilithium (not dissimilar from the Fleet Stores which charge Fleet Credit and Dilithium). I'm not sure what the "proper" price would be but if I were to choose I'd say something like 15 Omega Marks and 4,000 dilithium per weapon.
○ The Mk X Ground Sets should be available at the ground vendor as DOFF missions that take the same inputs as the current projects and only reward the specific piece of gear - in general just turning the projects into DOFF missions.
○ The Mk X Space sets should be available at the Space Vendor as DOFF missions that, just like the ground sets, take the same inputs as their current Reputation Projects do.
○ Additionally if the STF store is reopened it would make sense to add the STF DOFFs back and make them purchasable for a set number of Omega Marks.
The second suggestion is tied rather intrinsically with the first - to lower the entrance requirements for Normal STFs to Level 40 or 41. This is primarily to entice people to play Normal STFs and acquire and use the Mk X sets, but it always mystified me that players gained access to Normals just one level below the minimum level at which Mk XI and XII gear can be equipped.
The third suggestion is that the Omega Reputation be given Mk XI and XII Anti-Proton space weaponry store unlocks. I know the reasoning behind the removal of the anti-borg space weaponry and I'm not asking for that to return, but for special "Omega Anti-Proton" weapons in the same sense as the Romulan Reputation system gives us "Romulan Plasma" weapons, by giving them a second (or perhaps a first seeing as these are Anti-Proton weapons) proc and maybe tweaking the coloration or visuals of the weapons fire. Some ideas I had for the proc were Plasma DoT, Radiation DoT, and Antiproton DoT. The dev staff might have some better ideas though - I'm not so much attached to a specific proc as I would just like to see space weaponry added.
The fourth suggestion might be the easiest to implement - Faction specific anti-borg weaponry. Phasers for Starfleet and Disruptors for the KDF. Next to space weaponry, the ability to have anti-borg weaponry in two different damage flavors without needing to have one of the set weapons, is the most missed aspect of the old STF store.
So, just my two cents on what I feel would make the Omega Reputation system a bit better. I do have more ideas for it, but most of those fall under "Wouldn't it be neat" or "Wishful thinking" to a greater extent than these.