Major reworks were needed for a number of systems.
NPCs didn't do very well in mixed control scenarios for sex and companions made it worse, after the sex rework NPCs were a bit better in terms of trying for more varied acts but companions were even worse often choosing to quit or do nothing.
Combat encounters were really only balanced for solo player, bringing a companion often resulted in just getting a free turn while companion acted as a meat shield, after the rework companions were worse again being either a second god tier combatent or completely ineffective.
Well, that's because special NPC's had to be "super special". There is no reason why character X would work , but character Y would not if they use the same underlying system. They are effectively interchangable.
Companions were problematic for different reasons - IF you wanted to include them in every special scenario, you had to account for them. However that was never necessary. They don't have to take part in every scenario.
Also, balancing around them I guess, but that's isn't a real reason, it's an excuse. Of course companions effectivenes will depend on the level and build - like in EVERY RPG EVER MADE. LT isn't special in that regard. Again, other games find ways to deal with it. And who said balance had to be perfect anyway? Good enough is good enough.
And why wouldn't you have a companion? Going alone is just DUMB. Brinign your favorite slave, lover or daughterfu along sounds great.