I never liked Defender either, but then I finally got into it in some depth during Yolympics and now I think it's seriously awesome. I admit I haven't played it since then, but I'm gonna be hitting it hard during CAX this year with real controls. Give it a few hours and the learning curve might let you in a little...
Junior and Tron are both problematic games that I nonetheless enjoy playing. And the Tron cab is top 5 among all time greatest cab designs (EDOT being number 1 on my list), so that has to be worth something.
Echo the sentiment on Frogger. I respect the game, but I don't like playing or watching it.
I would have to defend fighting games to at least some degree though. They're not as similar as shmups are similar! SF2 Turbo is quite separate from an MK game, and both are a totally different experience than, say, Tekken 3.