I actually agree with the OP to a certain extent. I'm currently leveling two consecutive crafts and they really just aren't fun. I'm doing them because I'm being indirectly forced to.

The way I see it, the fact that it isn't fun in other games should be even more reason to try to make it fun in this one. I don't think there should be an "auto-craft" system though. And it definitely shouldn't play like bejeweled. But I feel it should be "mini-game like", in the sense that it could be short, enjoyable, and addictive. Different items can play out like different little "stages" or levels. There really is a lot of potential here.