Hmm..
I guess Beefheart is a good example, I heard Trout Mask Replica years ago and thought it was just a racket, just a bunch of people playing different songs at the same time, and then I heard Decals, which is like Trout Mask but a bit sparser... and I thought it was brilliant and I went back to Trout Mask and realized it was brilliant as well. Truely bizarre, and I've rarely found anyone who liked Trout Mask the first time they heard it (though I think one of the reasons I disliked it was the production, which is TERRIBLE; one of the only albums to consistantly give me a headache thanks to Zappa's lifeless production, yuck).
I can definitely see Pere Ubu taking a little while to like, you hit the nail on the head by mentioning all the hidden intricacies that make it work so well. I agree with a lot of the bands you guys mentioned taking a while to really enjoy -- definitely Unwound, Mission of Burma -- except perhaps Animal Collective (nothing too wild about it in my opinion, I latched on to the cool sounds and beautiful melodies immediately and I'm sure most of America will soon) and Unsane (amazing from the get-go! Though Cutthroats 9 are [were?] better..).
Ah, oh... BLACK FLAG took me a while to get into (rather, I'm getting into it currently), some guy made me a CD that he called "Black Flag's greatest hits" and it was a cut or two from all their CD's, and I remembered spinning it quite a bit and not really getting into it; a guitar part here or a lyric there would stick with me but it wouldn't really matter to me. Reading about microtonal guitar solos and Greg Ginn finally made me interested enough in Black Flag to hunt down thier albums and while I still probably don't appreciate them as much as I should, I'm getting there.
Everything I've heard from Einsturzende Neubauten has done nothing for me, but everyone I know whose opinion I respect has cited them as a favorite or an influence, so I could see myself end up digging them one day. Hmm.
Sway, all the early Pelican stuff is indeed awesome. Australasia is amazing.
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