But i still prefer a version where the borg are running around unnoticed on basestars, (see, i learned something ... or wasted storage room, not sure yet) like some insects walk freely into an ant colony and wreak havok there because the ants cant distinguish them from their own folks, so clearly
Oh, just because the Cylons and Borg are in an alliance doesn't preclude Cylons or Borg drones being on each others' ships. If anything, it would be a useful trait; Borg drones on a Cylon ship (though prevented from assimilating technology) would provide enhanced communications and command&control functions within a combined-force fleet of basestars and cubes.
Oh and one last thing about ST time travel, there a few voyager episodes where some federation time ship tries to destroy them because the federation believes that voyager will cause an explosion that will destroy earth.
So they do have the technology to travel time like space (or will definitly have because they have visited voyagers time) and the will to use it against a thread. (like some renegade romulan destroying the vulcan home world, for example ...)
AFAIK that would be 29th century Federation, which is pretty much an unknown and thus unquantifiable. The only things we really know are that 29th Century Federation peeps have a Temporal Prime Directive (likely what instigated the whole "blow up Voyager" stuff) and timeships. Other than that, we know squat.
However, I'll note that it's possible that the timeship sent to take out Voyager may have been sent in order to prevent future pollution of the timeline (by virtue of following the Temporal Prime Directive), and it's likely that if 24th-century UFP tried to use time travel to win a conflict, 29th-century UFP will show and say "you can't do that, suck it up".
From the Cylons point of view this new species, that has entered their universe, who are more machine than human, an alliance would hasten the destruction of humanity. The Borg would assimilate Cylon technology, if not the Cylons themselves. Did they not assimilate Federation Tech to defeat species 8472. The Borg would have drones on Cylon Basestars, adapting and improving all systems. I can see BorgCylon hybrids on Borg ships, Centurion chasis with the Borg fleshy bits being lower from the ceiling alcoves al a Borg Queen. An alliance it is with integrated systems on Cylon and Borg ships. Now to the Shadows.
The thing is though, that the Borg aren't more machine than human; they're part machine, part organic, but for the most part, they tend to not be human.
However, a Centurion w/ Borg fleshy bits would actually be inferior to the Cylon-standard Centurions, because it has those soft fleshy bits, which constitute a weakness. Centurions are already far and away superior to Borg drones; they have heavy armor plating, built in automatic weapons, and hand-to-hand combat capability that is extremely deadly against an actually militarily competent opponent (the Twelve Colonies).
Centurions are also at least moderately capable on their own, and also fairly quick to respond and move. Unlike Borg drones, which semi-mindlessly walk about slowly and have poor reflexes and very slow reaction time.
Also, AFAIK, the Borg had to use Federation technology, but did not assimilate it. They required Federation expertise to use said Federation technology. It's not unreasonable to think that this would be even more the case when the enemy is pretty much un-assimilatable.
