It's funny because Skunkworks isn't just my favorite Bruce album -- it's my favorite album period. By anyone. That's because I spent a ton of time listening to it, and it slowly opened up to me. I was attracted to it because it's such a personal album. It's like Bruce said, "Fuck my fans. I'm making this album for me." I find the songs honest and vulnerable. Bruce bares it all the way nobody else I've ever heard has. At first, I didn't get it, though. The album's almost entirely in metaphors, and I had to figure out what he was trying to emote lyrically, but as time wore on, it just all came together. Not only could I figure out what Bruce was trying to tell me about himself, but I was able to relate it back to myself. It's a very introspective and artistic album. But I understand why it would be difficult to get into. Like I said, I spent tons of time listening to the album, and only after that many listens did I start to fall in love with it. I'd say keep the door open with that album. You might enjoy it more down the road.
Jerusalem is excellent, isn't it? My favorite Bruce song. I'm surprised the rest of the album (barring the title track) didn't do much for you. Have you heard Tyranny of Souls? There really isn't a bad (or even mediocre) tune off that one.