I'll start addressing more of your ideas and issues once the holidays are over. I wanted to get a few things taken care of before then, but hopefully I can start to keep up more frequent official releases.
Since you'll be working on things over the holidays, I figured I'd throw a new suggestion into the mix.
By that I mean outputting DMA, HDMA, IRQ, and NMI events. Geiger's debugger does this (except for IRQ I think) and it is extremely useful. It gives you a quick snapshot of what is going on during a frame and between frames without having to dig into the code details. It also gives you quick and easy offset starting points when trying to reverse engineer various happenings. Lastly, the H/V counts provided show when transfers are happening and whether or not you overran your hblank/vblank time. It saves much time to see all of that stuff at a glance. I didn't see any way to do these types of things in bsnes-plus.