1. Never happened to me so I can't comment, but you can always create another new user of the name you want and it'll make a new folder. Move your stuff to it and change any permissions needed.
Given 2-4 are already sufficiently handled, I'll leave them
5. Don't use default (iCloud is a security risk anyway; I only use for
bookmarks, etc. I don't care about)
6. Don't use iCloud (security risk anyway)
7. I've tried to duplicate; all apps I've tried work from desktop here. An index.xml file missing sounds like it's typically associated with PAGES and NUMBERS from Apple according to a Google search. What program are you referring to that is having the problem? Clearly, not all applications have an index XML file so I don't see how it could be ALL applications not running from desktop. They probably have a bad pointer somewhere that expects to find it in a fixed location rather than relative to the application's own hidden sub-folders. You could look for the file manually from Spotlight (I don't use Pages or Numbers and I find no index.xml file on my entire computer so I have no idea what else could use it). I have Microsoft Office 2011 here and I've had no issues in Mavericks thus far.
I think this post on Apple Forums might explain the error better, though assuming it's the same one:
By default, Numbers '09 creates files which can't be opened by Numbers '08.
This feature has two explanations:
(1) Numbers '09 introduced a lot of features which are ununderstandable for Numbers '08
(2) the default file format is not a package containing a zipped Index.xml file as it was in Numbers '08, it is a zipped (package containing a non-zipped Index.xml file) whose extension name was changed from zip to pages.
Replace it by zip and you will be able to unpack it with a double click.
But given explanation (1), even expanded, Numbers '08 will be unable to open it.
Yvan KOENIG (from FRANCE dimanche 25 janvier 2009 14:50:19)
If it's some other program, I can't tell since you made it sound like every single application you've tried gives that error when run from the desktop and that makes no sense.
8. Mail DOES suck lately; You could try Thunderbird instead (and Firefox instead of Safari; later has SSL bug as of this posting and is unsafe anyway)
9. Never used; can't comment
10. Again, Mail is buggered right now. Again, I suggest trying Thunderbird where I've never had any problems (I have both ready here). In Mail, you can edit SMTP under Preferences/Accounts, however. I can even send responses from one account (e.g. Yahoo) from another (e.g. Gmail) with the appropriate selection. I have no problem changing the selection here. If you're expecting it to do it automatically, that may be your problem. Try Preferences/Accounts where you can access the SMTP server list settings directly rather than the drop-down "Accounts" where you can only create a new one. One is a Mail feature and the other is a system-wide settings feature.
Frankly, most of your problems are either taste issues, you're doing something wrong or you don't have enough knowledge of OS X to resolve what are relatively simple settings issues (or easy to find answers with a simple Google search). It's fine to ask for help, but concluding it is the worst OS version ever doesn't reflect reality, IMO. Anyone having what they consider a big problem in any OS version is going to be angry and blame it on that OS. It's clear you've already been there with Windows and now OSX isn't automatic/simple enough for you either. Perhaps an iPad would be a better choice if you want an appliance rather than a computer?