I'm not sure what the best setup would be, but I was thinking a folder/directory type deal for each character that you can open and view/save/load all saves for that character (Auto-saves not included in the folder/directories). This would be useful because I've had a few corrupt saves (due to mod issues), and I want to play those files again, but they are too messed up/won't load. I've also saved over a file (auto-save has saved my ass multiple times) many times. My friend just saves all the time, and has EVERY save in the save/load screen, which is nice, but WAY to unorganized for me.

So is this possible? Thanks in advance for the reply.

That behaviour's hardcoded into the game, I would think. Not something we can change.

Yup. As far as I know all that's hardcoded into the game. We can control when it saves (With autosave managers, etc), we can even rename the saves. But format, directories and method are all hardcoded and out of our control.

So if it is possible as above said to rename the files: would it be possible to have an alternative loading and saving screen?

Lets say: instead saving it into a different directory, would it maybe be possible to save it so that it is only virtually seen in another folder? in real the savegame would be in the same folder as it is now, but the loading screen would shows it in a different folder? This could be done if the savegame is renamed instead of ".ess" it would be renamed to "-.ess", and then it would be show in the loading screen in a different folder without that the files are in real in a different folder.

There should be some save file managers around by now. You might check on nexus and the like. External programs, but better than nothing if your juggling multiple characters.

http://skyrim.nexusmods.com/downloads/file.php?id=1840 has save management features that work similar to what you described ... they also remember which mods you have enabled in each save Profile...