Personally I don't have a lot of complaints about the quality of the game. Sure there are bugs, but that's to be expected in any software project of this size. When I find a bug, I report it and keep on trekkin'. (Reported one yesterday, and it was # 965,000-something. I wonder if they'll have a prize for bug report one-million.) :) Maybe I'm a glass-half-full kind of guy, but I enjoy the game.
As for the canonicity of a playable Borg faction, I think they could tell a story that would allow for it. In TNG's BOBW, the Borg created Locutus because they had a need for a spokesperson to interface with the races in the Alpha Quadrant. They adapted to the situation in order to meet the goals of assimilating Fed species. So who's to say they wouldn't adapt at some point in the future to include some sort of individuality in ship command, if the situation warranted such an adaptation? It would be not much different than the local computer on a NASA space probe having some ability to react to situations, but being guided by the researchers back on earth for the main mission work.
Barring that, it could be a rebel faction of Borg, separated from the collective, or a sub-collective that somehow got split off from the main hive mind. Maybe an off-shoot of the Lore-Borg, or the philosophical descendants of Hugh and company. Hell, it could be the bearded-Borg from the mirror universe. The point is, they could come up with a reason, just like they came up with the war between the Klingons and Feds for the game.