Looking at the midi 2.0 note on/note off messages, do I understand correctly that it still supports only 128 distinct note numbers? Technically one could abuse the 'attribute' to add extra numbers but that would be a manufacturer-specific extension, so not much hope for cross-device compatibility (and if you use the attribute for note number, where do you then specify the tuning information?). With so many other specs becoming better this seems like some kind of oversight. The topic of more than 128 note numbers comes up in microtonal/xenharmonic contexts much faster than in traditional music.
Note that direct pitch control per note does not really feel like a proper solution, as it will result in a single midi note number being used for addressing several frequencies, which (as far as I understand) makes it impossible to play 2 or more of those frequencies simultaneously.
Edited to add: this is not a "theoretical problem" anymore. As an example consider this device: http://www.shapeofmusic.com/overview.php
which offers 192 keys and currently has to work around the limitations of midi by using 2 midi channels to use all the keys.