The 2 big things I'm not happy about are the stipends & the new currencies.
I think this was handled poorly. Anybody who pre-ordered the game should be set to at least the first 4 days for each month (with Each day split up based on when pre-ordered).
2) The New Currencies
I think this was definitely no handled well. Introducing a bunch of currencies, many of which can only be found by chance and with a highly annoying, semi-complicated way of exchanging them (the new STF currencies).
Add exchanging of currencies (ie, a certain number of Rare Salvage for EDC's, and vice versa) . Add more ways to earn them, more STF's and Doff missions.