Maybe u using the infinite space mod :p, i know wat u mean, but then, its not the mod fault, i mean, i tell u, i didnt finish the game in normal mode with the borg cube cuz i was just testing, but i was already in sector 5 and nobody should be able to stop me..
I was using the infinite space mod as well, but since i noticed i coudnt test propertly the mod in the default game difficulty, because the enemies in the infinite space mod are harder than usual (i hate those boarding parties already in the first sector.. i die a lot of times because i cant stop a 3 mantis party lol..), i just removed the infinite space mod and i just made a little mod disabling the fleet pursuit and thats it. But trust me, if u cant advance with the borg layouts, then u will not be able to even reach sector 3 without using the inifinite space mod... its very easy to reach sector 3 with the borg ships. Those problems u are referring to are present in any ship/layout u play, i dont see the difference, its not like i changed the game mechanics or something

, the only problem u have to worry about is that u dont have shields, but dude!!, u have super strong hull resistance, u have 2 repair drones (if u think they are useless then definitely u must learn the basics of the game before... ), u repair hull damage everytime u collect scrap, u have higher hull points.... and with 6!! crew members u can do almost anything u want (repair, manning, helping repairs, fight, etc)!!! wat else do you need lol??.. dont try the bioship then, cuz its even harder...

As i said, i think u are doing something really wrong when u play, maybe u dont know some basics of the game, maybe u are not targeting the enemy weapons, maybe u are not manning the systems, i dunno. If i remember, the borg cube has the Beam, tjat pierces through 1 shield. All the enemies in the sector 1 have 1 shield. So u will reach for sure sector 2. Of course, playing the normal game. The infinite mod can give you a 3 shields enemy just in the beginning, i know that. But the problem is the infinite space mod is the one that need to be rebalanced (it can be too hard at the beginning, depending on your luck), not the borg ships... dunno if u know wat i mean.