First of all: sorry for the delayed response, I will always take a few days to answer because of school and the fact that I’m a lazy fuck. Again, sorry.
Second of all, and to answer your question: I will always love Daria and Jane’s friendship but I think it took them a long time to fully recover from “The Tom Situation”, as I assume it must be. But they handled it well, especially Jane: she realized what a great deal Tom and Daria had in common, that they actually made sense together and let them be. Granted, she and Tom were over by then, but it mustn’t be something easy to admit.
Third: And this is kinda unrelated, but I don’t understand why some people hate Tom. I know everyone loves Trent and everyone wanted Daria and him to be together but one of the best things about the show is that they never went there, it would’ve been weird and icky. Tom had to put up with Daria’s (understandable) insecurities and inferiority complex, and he really understood her and supported her. He wasn’t perfect, obviously, but I think the animosity is unwarranted.
Those are just my five cents.