Exodus has a good looking screenshot, I like the window with all the registers showing especially if it updates in real time (actually only if it does!) and 'All M68000 opcodes' is interesting as a feature. Does this just mean it can process them all or is there more to it?
The debugger of Exodus is likely the best among MD emulators. Yes, you can see registers, RAM, VRAM changing on the fly, you can trace VDP calls. Its active disassembly disassemble the game while you play it, thus discriminating perfectly code and data (normally, you can recompile the game after that).
It's almost perfect. It has 2 severe flaws though :
* its interface is heavy : you have to open many windows to make it usable (and AFAIK you're forced to navigate between menus to do that) and you end up with many windows overlapping each other, especially if you have a small screen (I work on a 12" netbook).
* it's SLOW !!! I can run it at 3 - 4 fps with the debugger !
I read on about Regen but nothing jumped out at me: 68000 debugger, 68000 overclocking and Many other features were all that caught me eye (further inspection about the chip emulation is interesting but on an unrelated note). Is the debugger worth checking out?
It's debugger is a little less powerful than Exodus', but all comes in one window, and the emulator itself is much faster (up to 100 fps with my weak PC).
Its main default is that there are some bugs, in emulation (program crashes from time to time) and in debugger (a watchpoint often breaks after the instruction that caused it, sometimes it corrupts RAM, watchpoints on RAM can't discriminate between reads and writes).
Anything about them in particular you think really sell them?
Both are said to be among the 3 most accurate (the 3rd is Gens).
To be honest, there are lots of features I'd have liked to see implemented in them, but since they are closed source, it's a little delicate to bother their respective authors (have they been open-source, I'd have tried to do them by myself before contacting authors). It seems that Regen's author is unreachable also.
That's just i didn't find anything really awesome for the MD (as I said, I had a bad experience with Gens, but I'm sure it's woth another try) for hacking.
If you could implement a basic but comfortable (this quality is often overlooked) debugger such as the one of Regen for Gens, I think it'd be a really strong base upon which you could develop interesting features (I have a personal list, but FCEUX or the NO$... emulators are full of ideas).
I have a similar project than yours (but not immediately : I'm very reluctant when it comes to code GUIs

) and be glad to see your work going
Good luck with your project !