Allow me to paint you a picture: An entire fleet of destroyers whose medium weapon slot is taken up by boarding modules is backed by a fleet of Light Cruisers whose medium weapon slots are exclusively EMP weapons (except for two ships that showed up late to the refit party and have nukes; handy just in case.)
This fleet also has a Heavy Cruiser armed exclusively with Defense Turbolasers. There's also a scout; he didn't do much.
So, this fleet is blocading a pirate world. They already blew up the space station and the defenses, but there's waaaaay too many militia and infantry divisions down there for me to take out, so I'm waiting to build up an army.
As I'm building my army, a Battlecruiser spawns in this system under pirate control. I would like to know exactly how; they surely did not build it on that planet I'm blockading, as my ships would have literally nuked any such things under construction in orbit, and you can't build anything bigger than a Destroyer on the surface anyway. But I digress.
Anyway! A Pirate Battlecruiser OPWagon shows up, and I think, "Hot diggy, here's my chance! I have enough EMP missiles to spam through his defense primaries and I can capture a ship just laden with tech ripe for reverse-engineering!"
I should point out: I am playing humans. The race which is supposed to jump at a chance to yarharrr onto an enemy ship, cutting down the crew with laser cutlasses and whatever.
I attempt to do so. My ships have only minor difficulty blasting this thing with EMP missiles, keeping it thoroughly locked down after the first turn, when it wipes out two of my eight destroyers with its non-defensive Primary Beams. However, at every turn, the crew of this Gremak Pirate Battlecruiser inflict considerably more damage on my ships's crews in the boarding attempt than my crews do to them. Nevertheless, I get it surrounded, and even EMP it so immobile that my Heavy Cruiser is able to reach boarding range and attempt to board. The higher crew of my Heavy Cruiser nevertheless avails them of naught, they simply take far greater casualties in exchange for inflicting a paltry few.
Nevermind! I have Defense Lasers, and I begin to carefully scythe into that ship. It's been EMP'd into insensibility, so surely I can just cut the crew down with precision laser strikes, reequip my destroyers' crews from the light cruisers' complements, and finish the job next turn!
And it's a great plan, with just one minor drawback. The Gremak's turn comes, and the bastard self-destructs!
What, exactly, was the point? This was pretty much the best reasonable-case scenario: an entire fleet designed for boarding jumping a single ship; a large ship, but still one ship. And it "wins," in the sense that it was able to blow up two of my ships and itself rather than be captured. And I'm playing the race that's supposed to be capable in boarding actions!