Something that I see lacking in the main client is to be able to determine a fee on the fly instead of going trough the preferences to change it and return it to normal.

I am all in for the folder structure.

Based on some patches made to the main client and forks this are some ideas to implement:
-Import Keys
-Determine where the .dat and important files would be located
-Deterministic wallets generated with a strong password. No need to store the keys in the wallet.dat(16+ chars cap and uncap, numbers, and symbols)
-Vanity Generator, Miner, and bulk key generation.(Under a certain folder x ammount of keys)
-Show addresses already "linked" together in groups.
-Advanced Send(From, to, both with multiple inputs/outputs and a specific fee)
-Access control for the API, create users who can only manage specific accounts and/or limited commands.

For usability make a divide between: Power Users/Simple Users.
Power Users have low level access(Many of the futures described above)
Simple users are limited to tx historial/contacts/send and status/messages dumb down.

Will help as I can when I get my Ubuntu box set up again.