BWL was easy enough attunement, problem was people not knowing if they had done it or not prior to raids, then holding a raid while 5-10 all of sudden realised they hadnt done it yet. Then factor in the Onyxa Cloak problem meaning progress was delayed for so many ony kills before you could continue in BWL. Vanilla was really just a farm/grind though to get into raiding, not overly hard just long or boring.
Edit : I didnt make it to Naxx vanilla so cant comment on that part of vanilla.
Problem with both Vanilla and TBC was poaching of players for other guilds. lower guilds geared/attuned them and then they hopped ship so quick and often it became a problem and guilds disbanded over it. Another big problem was how prized some items were (Dragonspine throphy, Aldori Legacy defender (gruuls shield?)) that people made too much of a deal over them, but there was no real alternatives available. Atleast now there is alternatives available even if a little below BiS.