I had some trouble with Joe's Garage at first, too, and this was after I was already a Zappa fan. I was a major proghead by then and thought "Really Frank, a concept album?" The whole thing being narrated by The Central Scrutinizer was wacky, but not itself a horrible idea. It actually kinda worked, because as with most concept albums, you do need narrative to tie things together. The whole homoerotic/mechoerotic thing with Gay Bob and Sy Borg was weird and frankly a turn-off. It didn't help that I'm 100% straight (sorry dudes) and some of my friends took to calling me Gay Bob "to be funny". The episode with Joe from work didn't really help, either. (Weird, his name was Joe. I never thought about that before, although to this day, when I picture Joe from Joe's Garage, he looks like Joe from work.)
But eventually I realized that the story of course was insane as only Frank could do it, parody of the highest order, and the music as always was great. The story seems to get a bit lost in Acts II and III, but the solos... wow. And since the music is always more important to me than the concept anyway, I ended up liking it. But as with most concept albums, I have my favorite parts and rarely have time to listen to the whole thing, and just listening to individual tracks seems somehow wrong. Which is dumb, but there you go.