My biggest request by far is to have some sort of centralized permissions system for which groups have access to different functionalities of plugins. This permissions system would allow both user-specific and group-specific permission configuration and would mitigate the amount of small, permission-only plugin admin pages.
This could be done by adding the hook filter:permissions.addFields and then doing something like the database module to get permissions of a certain user or group. This, along with a simplification of settings, would be super helpful for easier creation of plugins. Plugins are going to be the best part of this platform, and if they can be created with more ease, then this platform will be embraced more. This could be done via a plugin, but it would be so much better if it were included in the core.
Client side features requested:
API for accessing certain server-side functionalities. Post parsing on the client side (so I don't have to include markdown.js).
Also, I should mention that after I'm done working on the 5 or so plugins I have in queue, I'm planning on developing a very strong polyfill server-side module library for bringing all browsers up to standard based on user-agent (to minimize unnecessary code).