Krikzz only mentions automatic region detection for the CIC clone and a better shell. Hopefully a custom region-free shell. It was determined previously that save states isn't possible (or very complicated) to do via the cartridge port, so don't get your hopes up for that. Probably not much reason to upgrade if you already have the v3. I might upgrade though since I only have the old v2.0 that came with donor 6102 CIC and donor shell with a crude handmade SD slot.
I don't think things like 64DD support are restricted by the hardware (other than the fact that it's a flashcart and not a complete 64DD clone), so I doubt the new Everdrives will improve the possibilities for these things, but who knows.
The thing with MSU1 is that it allows streaming data like CD-quality audio and video on a SNES. The N64 is already capable of that so an MSU1 makes little sense. But sure, if someone comes up with a new cartridge hardware feature that can be used by homebrew and hacks, it may be done in the FPGA. Possibly not very likely to happen anytime soon though considering that the emulation, hacking and development scene for N64 didn't really take off until quite recently (which we have the Everdrive 64 to thank for).
