some of the things mentioned could be done by simply extending the
midi specification.
for example, if one needed a higher resolution for a note-on events velocity,
the event could be followed by a sysex data with one or two additional
7-bit values. (kind like it's already done with MSB and LSB for some
controller values)
sequencers, that supported the midi extension would provide a flag or logo:
midi OX (midi open extension)
a complete new definition would likely be more clean
but less supported, since midi is already build-in in hard/software
and could more easily be adjusted to send,receive and handle the
addition info.
afaict midi doesn't say anything about frequencies, you could map the
middle C nr 0x60 to any frequency you want
there's just no consensus/spec how to do it, how to handle it, how to
tell/inform other apps about it, etc...