I love the usability both on the frontend and with the api. So much thought has gone into how people actually use the software. The ability to easy copy template id's is a lifesaver. I know it seems small, but it brings the use-ability up to 11.
There frontend does not always update as if the page was refreshed. Sorting is a good example of this. Things are sorted alphabetically when you refresh, but not so when you update things on the frontend.
Email templates always look ugly. It's really hard to organize your html in way that isn't overwhelming to nontechnical people. Also, would like to be able to access snippets from within the template editor. You currently have to have multiple windows or tabs open to manage snippets.
ALSO just thought of this! But versioned snippets? Right now if you change a snippet it affects all of your emails. I wish there was a way to create another version that you can test out before you publish it live.
Finally, a better way to promote versions when you promote new code that makes use of those new versions. There have been a couple times where this has been missed because it is an extra task.