Fear not, people cowering in fear from the might of the ‘OP Battlecruiser’, I have a solution for you!
Firstly, let’s analyse the situations in which you will discover an enemy BC (this is assuming you are 100% scouting your enemy at all times, like a good player should, if you’re surprised by and BC you’ve already lost).
If your opponent is rushing battlecruisers, just wipe him out, the amount of resources he has to invest in that thing early game will cost him the game, no special counter needed here.
The Actual Proper Late Game Appearance
Right, this is where they’re actually scary, I’ll put a TL;DR at the bottom, but here is a good explanation of how I’ve been countering these guys pretty successfully:
a) have the mothership/flagship on ‘stay docked’, fill with adequate numbers salvage corvettes (I like around 10). Do this before a BC is even on the field, just have it on standby, preparation is key. To avoid unnecessary launch micro, just have the MS building capital ships, like it really should be at this stage of the game (leave your carriers to strike craft production). - Spotting an enemy shipyard is usually the signal to start this if you haven’t already done so.
b) as soon as the BC launches, jump your MS right on top/next to the BC and launch the salvage Vettes, preferably angle your jump so they come out really close to the BC (you need to be close for this to work). Jumping as soon as it finishes building for the most part works because the main enemy force will be on the front line, not guarding the shipyard. Use common sense here, if there is a scary armada guarding that shipyard please don’t jump, wait for another opportunity. I will discuss Gravity wells further down.
c) the moment you have 6 salvage vettes latched onto the BC, he’ll INSTANTLY CONVERT! This is because BC’s are too big to fit in your MS, so it’s a simple case of if they’re close enough to the MS they’re instantly yours.
d) you now have a fresh Battlecruiser on top of the enemy shipyard and most likely mothership too, enjoy.
^This will of course not work if they are using gravwell generators. If the GW is on the enemy MS/shipyard, wait for the BC to clear the no jump zone and hope you can get him before he meets up with his fleet, or just make sure you keep killing enemy GW’s with strike craft when they build them if you are able. If the BC builds its own GW, kill the hard point with a swarm of interceptors and bombers then proceed. If the BC is with a fleet when you finally have a chance to jump on him, don’t do it unless you can send your own significant fleet in too. If this does end up being a proper engagement, even if you lose a destroyer or two before the BC is taken you’ve still just stolen their most powerful ship, and it’ll turn its guns on his friends with haste and cut 'em to ribbons.
If he has more than one BC with a big scary backup fleet, it’s already over.
TL;DR: fill MS with salvage vettes and jump the MS right next to the BC, launch them, as soon as the 6th vettes latches on its instantly yours, no travel time needed