A wishlist for two categories, in each sorted from very important to less important:

Technical:

• Open all links relative to my home instance (I want to stay logged in)
• Make community discovery easier and consistent. One method, which always works.
• Move account to another instance, complete with subscriptions and notifications when older comments receive replies
• Clarity: I'm often confused in which community a post lives, or where it originated. Or what a user's home instance is. It is fine to display relative information (Post X from instance Y as seen from instance Z), if clearly less emphasized
• Indicate who can see a post or comment. From what instances is that content visible?
• Display the same community stats regardless from which subscribed instance they are viewed (subscriber count varies wildly)

View:

• Allow to hide selected posts
• Expand and collapse images in threads
• Lock my feed: Please don't add posts to the top while I'm browsing the thumbnails at the bottom
• Display post/comment live preview below input field, so I can see the preview while editing. Currently I must switch view.
• Search within a community (without leaving the community page)
• Customize your feed: Control how much of each community is displayed (I want posts from some small communities to always show, and posts from others to only show rarely, or only those with votes/comments)

This was meant with the web/browser in mind. I expect apps and clients to work similarly, unless a characteristic necessitates exceptions (screen size, touch, ...).