I've been with STO since it's release and become a lifer one year later. I play the game almost daily, especially since the release of the DOF system, and I'll run a few STFs...and like you I haven't been lucky with getting STF gear. I have managed to accumulate close to 300 Encrypted Data Chips and managed to get what I can with that, but it seems impossible to get the elite gear. The same goes with Lock Boxes, I spent a lot of money and trading dilithium for Cryptic/Zen Credits to buy master keys in the C-Store and I have yet to get anything really good or rare from the Lock Boxes. I have a lot of Lobi Crystals, some Fleet Credit Pool bonus (and I'm not even in a fleet) and 8 Mirror Universe Starships (which I have no room for and don't seem that great).
Now I know random means random, but I'm sure there's a way the game can see how many times a player has run the STF and can increase the chances of receiving more very rare/rare rewards upon completion.
I have hundreds of Cardassian, Ferengi and Tholian Lock Boxes stored in my banks and hope someday to score one of the very rare ships and other gear, once I eventually buy more master keys. I only hope the very rare items are not take out of the lock boxes I already have once the drops are over?
I'm also a lifer, bught the preorder, BETA/Early Access...all that jazz. I got my Borg gear back when it was free for finishing the mission (yes, STFs were assigned as missions). Now that they put in the MACO and OMEGA stuff, I have done 40+ of each STF only to get 1 MACO rifle, 2 MACO armors, 1 OMEGA armor, and NO OTHER TECH. I bought the MK XI's with EDCs (obviously) but I've given up on the Elites.
Honestly, it's easier to grind for enough EC to buy master keys and open enough lock boxes for Lobi crystals than it is to get endgame gear. I JUST bought the upgraded Crystal set. It took about a month to grind for the lobis to get it. STF gear is an all or nothing deal. I say don't bother.
The 1000+ DIL for completing them is nice, and that might be enough for most. I personally avoid them unless I'm really REALLY bored.