Copy a large file to USB drive or transmit a big file via LAN and the machine will either freeze or become "jerky".

This is because the IO is blocking the CPU. It's a kernel problem that has been around for ages and it's time to sort it out for once and for all.

http://en.wikipedia.org/wiki/Priority_inversion
http://en.wikipedia.org/wiki/I/O_scheduling

If you are copying large amounts of data in Nautilus or something, or you're installing some software then the computer gets very slow to use while it is doing that. You just hear your disk chugging and the computer is slow and unresponsive.

I propose that set the disk I/O priority of file transfers (Nautilus), Synaptic and Update-Manager to one of less importance.

Copying files is an time unimportant process. It is done when its done. It shouldn't use up all disk bandwidth when you are trying to do something interactive with the computer.

If we change the disk I/O priority for certain processes, it will result in Ubuntu being much more responsive and useful under heavy load.
If you're not doing anything interactive while copying the files, the transfer would run at full-speed and still be just as fast as before.

I think it'll be a good idea to have a disk that repairs system files on an ubuntu crash (rarely occurs, but still needed) It'll be very helpful as a repair option instead of reinstalling after formatting the ext2 partition and losing data.
These disks are available for Fedora and in Windows Xp, the installation disk has a repair option. Hope the developers will consider this.

Currently, the progressbar in usplash is updated by the initialization scripts.

Although this works ok, the progress effect is very ugly because the bar moves in huge increments and then stops for an undetermined time until it moves again. Besides not being beautiful, this provides no information to the user about the time remaining for the boot or shutdown process.

I suggest that the usplash progressbar be time-based, pretty much like the progressbar in MacOSX.

Since the booting and shutdown times do not change drastically from session to session, we could save the time the computer spent to boot and to shutdown, and use it to guide the progressbar the next time. This would provide a beautiful and smooth animation of the progressbar, and an accurate remaining time, increasing the usability.

This can be already implemented using the current usplash code without modifications whatsoever, and a working solution is already available.

Please check it here:
http://gnome-look.org/content/show.php?content=93386

Ubuntu PPA:
https://launchpad.net/~usplash-smooth/+archive

Ubuntu WIKI:
https://wiki.ubuntu.com/UsplashSmooth