I have not been to Bagan yet, but have seen pictures and heard stories that definately put it on my list.
Angkor region is amazing for the size and scale of temples over a wide area, it is a really special place.
I was fortunate enough to stay at Amanjiwo for 3 nights during my visit to Borobodur. Did the sunrise thing, and my wife and I were the only people there -- a bit different than anything around Angkor which was hard to find a place that did not have many people around. There is not much else in the way of significant historical items around, but a pretty amazing 3-4 hour elephant ride through villages and river beds back to Amanjiwo could be a possibility. Some nice hiking in the hills around this area is also a nice way to spend some time. Prayer time in the valley can be pretty haunting hearing the speakers from mosques in the region merging into a kind of disonent hum.
All are good choices.