1. In most cases you will have to edit the option out of the templates. Many of these have been done already and can be found in the template forum here at threadsdev. A few are changed in the config and theme pages in the admin area.
2. Yes, you will have to edit the templates to remove these.
3. It shouldn't be a problem since you would only need to have separate directories with the different template sets.
To remove the repeating the subject in every post would need some small hacking to accomplish. Depending on how you would like to have it, the script could remove the topic if it is the same as the topic of the post above it. Or it could just remove it for all, but then you should remove the possibility to change the subject as well.
The edit links needs to be next to the post to edit, otherwise you wouldn't be able to edit each post.
The reply is at every post because you are able to reply to any post that you want to, not just reply to the thread as a whole. You could of course cripple the program and remove these links and instead install the part of the quick reply hack that adds a reply box at the bottom of the page.
You only see the post you are replying to, since you are replying to that post and not the whole thread. It is a different, more detailed way of discussing that some (including me) likes better than a complete flat mode. If someone really wants this it shouldn't be too hard to include showflat in newreply.
You can change the size of the post textarea in the theme config on your admin page. Also, users can set the size of this box individually on their own control panel.
Regarding your thoughts on the move I believe that is the best way to go.
