All right, I made it to Mie finally!
I spent a whole day just in Ise and Saiku. As well as some of the more obvious sights in Ise, I also visited this museum (神宮 徴古館) which is probably as notable for the building as the collection. They do have some gifts that Toyotomi Hideyoshi and a few of the early Tokugawa shoguns gave the shrine though, which are kind of interesting.
I really enjoyed Saiku, the site of the former palace of the vestal virgin of Ise. The museum there is interesting, with various artifacts that they've dug up at the site, and models of what it all would have looked like. They also have a video of a re-enactment of a vestal's journey from Kyoto to Ise! She would have traveled by palanquin, apparently, with an entourage of some 500 people or so. And a common problem, at least in the 11th century, was that the good folk of Mie weren't particularly bothered about doing what the people in the Capital thought they should be doing.
I also went to Matsusaka and Seki. Matsusaka was surprisingly interesting, with a few interesting sites scattered walking distance from the train station. The tourist office next to the station produces a decent English pamphlet. Most of the sites are free, and at least two of them have buildings which are Important Cultural Properties (a large, sprawling mansion of an Edo/Meiji-era merchant family; and an interesting double row of late Edo townhouses, which were originally built for samurai guards of the castle and their families, and are today still occupied). The castle is interesting. The Motoori Norinaga museum is currently closed for renovation, but his house is still open.
Seki's a lovely post town in a scenic spot in the highlands of the Mie plains. The main road's about 2km long, and the majority of buildings along the entire road are 19th century. I certainly wasn't the only tourist around on a Sunday afternoon, but the place doesn't feel touristy. The train line serving the place is old school JR - single line, non-electrified, and with many trains having only one car. The route from Seki over the mountains to the west is very scenic - it's worth going there just for the train ride.