I just heard an interview with the sto dev that's in charge of STF set rewards. He points out that the system is designed with the following features:
A) The difference in stats between Mk XI and Mk XII is intentionally very small. Mk XII set is designed more to give players a unique costume/look rather than for stats. Mk XII set is really intended as a reward for very hardcore players who enjoys running lots of STFs.
B) Even with extremely bad luck, it is still possible to obtain a complete set of Mk XI with 120 successful runs (Assuming the player has the bad luck of only getting 1 EDC per run). In reality, most players will be able to get enough Borg salvage tech/EDCs to get a complete set after 40+ STF runs.
C) Cryptic's intention is to release a new STF costume set every 3-4 months. When that happens, the new costume set will replace the current Mk XII costume set. The current Mk XII set will then be obtainable using EDCs.
My thoughts are that if this is really their intention, then Cryptic should not have labelled the STF sets as "Mk XII". It creates a huge misunderstanding to the playerbase that "Mk XII" is better than "Mk XI" set. For example, instead of the Omega Mk XII set, call it the Omicron Mk XI set.
It looks like the Vault Shuttle set also follows the STF design where the Mk XII set is intended for hardcore players who is willing to run hundreds of Vault shuttle missions.