When a "serious" PvP'er builds out character, ship, gear and BO's, they always go for the cookie-cutter ultimate Flavor of the Month in order to be "competitive". There in lays the gotcha that could be used to make a counter-argument against the OP - there will always be a "best" weapon, "best" build, "best" ship, "best" group of BO's. No matter how much you tweak abilities, gear, ships and BO's, a min/max'er will always find the best of the best of the best, "with honors, sir" <salute>.
So if the changes will only really effect PvE, and PvP'ers will just go with the FotM, why bother with any changes at all?
To widen those choices and broaden the "act" of choosing into something more than just a small number of "FOTM" builds based on a select few powers.
Sure , cookiecutters exist in every PvP and PvE game because players go with what been shown to work.
Players also go with what makes them happy anf what they would like to play as well. Take smallsam's build for instance. HIghly uncookied and yet that player plays it almost exclusively. Turret boats are another good example of an unFOTM build not used by the masses.
The expanding of those powers that fall outside the FOTM into viable choices enlarges the field and helps widen the build base that can and will be used by the players in PvP,PvE and even as NPC builds in the UGC (if found to be intriguing enough). Make the choices wide enough and even though cookiecutters will still exist the options for those whom "think freely" now exists as well.