Yeah, I have to agree, as mediocre as some of the 90's era stuff was, it was still only based on the original trilogy, and the writers didn't have to deal with feeling like they had to tie it all into the prequel garbage, or retcon the hell out of the existing stories when the continuity started to go to hell. Not to mention the filth of the New Jedi Order and later things had yet to happen, so the name of Star Wars EU hadn't yet been sullied to anywhere near the degree that it has now.
Even Timothy Zahn, whose work I adore, hasn't been immune to this problem. It's very bizarre to hear Luke and Mara suddenly talking about separatists and droidekas when previously they had known virtually nothing about the clone wars era aside from the fact that the clones had been the enemy of the Old Republic. Frankly, I like that idea a lot more than anything the prequels presented, and in my mind Zahn's original ideas are how it 'really' happened back then. Also, Vision of the Future was such an awesome grand finale that it should have been the conclusion of the entire Star Wars story (and can still be regarded as such).
It just blows so much that the official publications have to be made to fit with each other, when that is becoming ever more of a joke and impossibility. I don't even think rebooting the EU would be any good, because then it would just have to start from scratch based only on the officially recognised material, which is the SE's and prequels, and wouldn't be true to the original conception of what Star Wars was all about in any way. Selective nihilism is the only way to go if you want to retain any enjoyment of the things that actually are good.
If some folks wanted to, say, write their own unofficial stories that only made use of the good stuff and discarded the rest, that would be brilliant; but then of course you run into the problem that 'fan fiction' has a bad name with a lot of people, due to most of it being written by illiterate thirteen year olds. Although it's an amusingly disturbing truth that the better fan-created works often surpass published material in quality . . .