I have no figures to back up what i'm going to say, only personal opinions and those of a few friends who felt the same way
I like most viewers hated Arnold Rimmer, everything about him was the worst it could possibly be, with basically no redeeming factors, and it was that HATE, deep and to the very core that made all the fans (myself included) LOVE the character.
Rimmer was exactly what everyone should strive to be in the work place, follow the rules to the letter make sure everything was done according to policy, be the model employee, but doing all of it just wrong or to the annoyingly extreme level.
Lister the polar opposite, the character that everyone should hate, who does all of the wrong things but in the right ways or at least in the ways that most people act (or wish they could)
Cat offerred the third point in the trinagle... caring only about himself the selfish (ooo Fish!) and "stylish" that most people can be and wish they were or weren't on any given day
Three sides of humanity summed up to their extremes, then entered Kryton... yet another side of humanity, the emotionally shy and unsure of himself, but is intelligent and underappreciated but still too shy to stand up and grab the attention.
It was now a square but each corner held up a partically part of the human existence in a funny and interesting way.
When Kochanski came on, the show the lost that balance, the series became an awkward will they won't they between Lister and Kochanski the shape of the show changed and no longer had that cornerstone of humanity. and that was so far removed from what the audience was used to that it was not received well, although to be fair even after Rimmer came back the series had lost its spark by that point in my opinion at least