From the top of my head...
tab-complition in the shell itself, so that it is present even when booting without startup-sequence.
Fix the pipe support so it does not need external pipe command
Something akin to xargs on unix built into shell (for example
http://aminet.net/package/util/shell/EArg)
Reworked prefs system. Something like a prefs.library with a companion program that can read, validate and translate text input to prefs files and vice versa. Add a rexx interface and anyone can easily create Prefs programs in whatever GUI toolkit they like, or stay with text files if preferred.
Fix the console-handler/con.device mess, improved ANSI compatibility, maybe tabs.
Improve the font system to handle current font formats (truetype) natively
(UTF8 would be a bonus)
Improved c:request#? programs.
Fix locale issues with C:Date, and give it LFORMAT option
Let system time survive "warm" reboots, even without RTC.
More Workbench screens, and possibility for WB windows to jump between them.
... :)