Actually, the best way to deal with a FB was to have a half elf bard with that Racial Substitution Level ability which duplicated a "calm emotions" effect (IIRC) with a DC equal to your diplomacy roll.
Dread Necro wasn't that bad for a 20 levels class. At least you got something at every level. Sorcerer only had...summon familiar..as a Core Class.
As for the 3.5 PrC, I just miss the variety. Because they were many a feats and prestige classes. The difference between some of them might have been huge, in terms of power level, but you had such great variety.
As far as I can remember, the majority of the PrC I liked back then were considered very bad.
I can't tell for sure if the archetypes was the best way to go, though I do agree that having to dip 5 PrC was something that did bothered me too.
I think you can make the character you like, either way, and if you're not into minmaxing anyway, you might not even care if your character is a bit (or quite) weaker than he should be.
And, really, you can't compare the "overpowerness/imbalance" of 3.5 with that of PF (don't get me wrong that's a good thing).
*Edit: Fighter also had , as most of the base classes in the later books, an alternative class feature, a thing like minor archetypes one might say, that had to do with crashing your foes into walls for extra damage. I think you exchanged feats for that. Come to think of it, fighter was one of the base classes used for a 1-2 levels dip.