I've been dealing with this and it's extremely frustrating. I've left my backup going all night only to wake up and have it only be 1/2 done.
I've basically narrowed it down to faulty/buggy apps. I just went through this over the weekend and I deleted every app (stopped it from syncing) that didn't contain to much personalization information on the ipad. I didn't want to have to go through and set up all of my app customizations or lose data on some apps I have so I kept maybe a dozen.
I've found that if I strip my apps down my backup goes down to just a few minutes. Now I'm starting to add apps back slowly. I think the problem may lie in apps that store a lot of data locally on the iPad. I don't know that for sure but it seems like that's what's going on in my case.
The problem I've run into is that I tend to load back up a bunch of apps (from my iPad) and I don't sync very often, so the next time I plug in in takes forever to backup and I don't remember which apps I installed last, so I start the process over
