About the only thing the Federation could do to counter the Empire is transport photon and/or quantum torpedoes to vital points like the reactor or engineering space on the Imperial ships, assuming it is even possible, other than that they would almost certainly lose. Yeah, the Borg could assimilate the Federation in a heart beat if it really came down to it, because the Borg have basically been toying with the Federation since Q revealed the USS Enterprise-D to them.
I'll point out that due to the temperamental nature of transporter operation, being able to transport weapons into the Empire's warships would likely not work. Oh, and ISDs all have super-dense and very thick armor, which is already known to be unfriendly to transporter operation.
Assuming the original mods put proper ships in the same roles as the original races, it wouldn't be too outlandish for a crossover mod to be feasible.
I don't think anybody's actually argued against this. Rather, the thread's veered off track.
Most alien species want to kill us or eat us.
The Borg they are different.
They want to take your humanity away and turn you into an obedient semi-automaton. This process of striping away your very being is what’s frightening.
The fear as they drill out your eye and replace it with an ocular implant without any anesthetic. The nauseating smell of human faeces, uncontrollable due to fear, of burnt flesh and bone, that lingers at the back of your throat and assaults yours senses, with the noise of 10,000 power saws and cutting discs that are removing limbs on an industrial scale, deafen you, causing your ears to ring and the screams and crying of children, so many children, as their flesh is violated. You may kick out with all your might; you may try to fight back but to no avail.
Resistance truly is futile!
And as the process continues you anticipate death.
But death does not come, you don’t die. The Borg nanoprobes they injected into you, start to accelerate your healing process, ready for the interface with the Borg technology, so that your body does not reject your cybernetically enhanced implants. The cranial transceiver that they put in your head starts to come online and at that split second you realise the horror. A life with passion, hope, love, sex(some of us)... is replaced with an existence of a vegetate servitude state as a Borg drone, with nearly 7 billion voices in your head, that within minutes of switch-over turns you insane.
The C’Tan and the Tyranids they just want to eat you, in one go, most of the time. No lingering pain. No assimilation. Death is almost instantaneous.
Anticipation of death is worse than death itself. That’s why the Borg are so frightening. It’s the threat of the forced assimilation against your will. To pick the lesser of the two evils, you can eat me any day!
I'll point out a couple of things:
1. The Tyranids are totally alien. You can't understand them, at all. Federation+Tyranids=NOM NOM Federation. The fear with the Tyranids comes with the fact that they don't care, that they are totally alien, and that they are pretty much eating things because they're hungry. Also, most Tyranids don't actually eat people. They simply kill you in horrible, painful ways, and then other Tyranids come along later and drag your grungy corpse to a digestion pool.
2. C'tan eat people, yeah. But the thing is, they do it slowly. And they don't actually eat people, per se, rather, they kill you and eat your pain and suffering, oh and your soul too. But not all C'tan are actually like into "eat and kill meatbags hurr durr". Some like to manipulate and basically mess around with humans, and make people their slaves. After all, they must have a supply of meatbags to kill/eat, right?
3. The Necrons, who aren't the same as the C'tan, are also different. Most Necron Lords pretty much are either borderline automatons or pretty loony. Either way, they go out and harvest, and/or kill meatbags. Why harvest? Well, you need to make more Necrons! Especially Pariahs, which are a special type of Necron.
4. The problem with the Borg, is that they aren't really that scary. Because eventually, they can be defeated. You can figure them out. They want to assimilate new races in order to grow stronger and assimilate even more. It's that simple. But, say, the Necrons or C'tan, or the Tyranids? Nobody really knows why they do what they do. I mean, you could say that they're eating planets and suchlike 'cause they're hungry, but no one really knows for sure.
Because the Borg have a Queen, who is actually capable of independent thought, they could, quite plausibly, be reasoned with. Can't reason with a robot-vampire-skeleton or giant spess bugz.
Also note that Borg are the archetypal zombies in space. And that, faced against most other scifi empires (Empire from SW, Imperium (or really any faction) from 40K, for example), they loose. HARD. Because either they're outgunned enormously, or they're outnumbered. Or both.
I'll also point out that 40K has species that are much scarier than the Borg. Eldar? They manipulate humans into dying by the planetfull just so a half dozen Eldar will live.
Dark Eldar? They go on slave raids to torture and pillage, because they've discovered the Elixir of Youth, and it happens to be the pain and suffering of "lesser" races. Oh yeah, and they like to do all sorts or weird, and deviant stuff. Like, vivisect people, or graft extra arms/legs/spikey bitz onto each other, all for "shits and giggles", as it were.
Orks? They just kill and fight, because that's what they do. Doesn't even matter if they win, loose, or run away, so long as they're fighting.
Tau? Sure, they seem like nice guys (join the Greater Good, and keep your religion too!), but they're really not. Sterilizing a human population isn't very kind, now is it?
Chaos? While they might not be alien, they're infinitely worse than the Borg. Why? Simple. Simply looking at a daemon of Chaos can cause terminal insanity (i.e. die from going loony), and daemons also tend to be nigh-impossible to kill, as well as very interested in killing other non-daemon things. Oh, yeah, and they like to eat your soul. Which in 40K, is possible.
So really, the Borg are by far, not the scariest thing around. I might be harping on 40K a bit, but really, it's because 40K has a lot of really scary shit in it. Because it's the grim darkness of the far future, and there is only an eternity of war to the laughter of thirsting gods. Forget the hope of the future and science, for so much has been lost, never to be regained. And no one will miss you if you die, for you are one amongst trillions.