The borg set nerf doesn't really bother me. At least the logic there makes sense, if I don't happen to entirely agree with the decision.
No, what gets me is the dil tax to upgrading/getting doffs. It makes little sense from where I sit, other than perhaps a dil sink. But now, barring other changes to the doff economy yet to be announced (the doff grind would be a lot less important if starbase improvements were scaled to fleet size, for example), you have to grind to grind to grind. STO is already pretty lacking in content; I imagine the reason most play after a month at top level is that shooting things with spaceships is so damn fun, and there aren't a lot of alternatives at the moment. And unlike a lot of the other changes we've seen so far, there has been no official even half-explanation as to the reasoning, as far as I know.