I'll try and cover as much as I can:
Can you please point to some (working?) sample of implementing a barebone default / dev setup (css, js, basic templates, custom fields, groups, users, matrix forms, front-end forms,...) using a plugin?
I don't think there would be anything where this is implemented with a plugin (unless i'm mistaken), but P&T have an installation of Craft you can either clone on Github or generate from their website called HappyLager, this contains a bunch of boilerplate to you get you started including sections, entry types, matrix fields, relations, assets.
I don't think there is anything with users on there though due to licencing, Craft personal only allows one user and Client 1 Admin and 1 Client account : http://buildwithcraft.com/pricing
Is there a way to "enforce" presence (installation and activation) of "related" plugins ("must use" plugins) so I can develop a theme with functions/features related to other plugins I do not own?
There is sort of a way to do this I believe, you would need to have a set of dependancies you could define as an array in your main plugin class, then when your plugin's CP/settings page is loaded, do the checks through a controller to see if the correct plugins are installed and proceed with notifications, errors when conditionals are met etc.
An example of a plugin i've seen that has done this is the Twitter plugin from Dukt, its free so you should be able to download it and find what you need.
TwitterPlugin.php is where the logic is (from what I can see) then
controllers/TwitterController.php to put it all together and then
templates/settings/_dependancies.html is how it's dealt with in the front end.
It might be worth having a read about plugin development: http://buildwithcraft.com/docs/plugins/introduction
But I think in your themes readme, a simple list of required plugins with links on how to get them would be good enough for most situations.
In craft I don't get the point / simply don't understand where to start just to add custom fields and relations
This should be solved or become apparent in the HappyLager demo? if not the documentation is quite helpful with this:
I also don't see how I could use a plugin to create a theme / copy the related files and have them "managed" by my plugin.
I think the problem with building a theme is there are so many factors involved with regards to how someone might have their backend set up (if retro fitting a theme) as you if you had something like
craft.entries.section('news') in one of your templates but the section is called
blog your theme isn't going to work.
For a clean install your problem might be with licensing, I'm not an expert on it by any means so if anyone else knows more information please edit this answer, but I would assume you would need to be careful how you add sections and users at the least.
Your plugin could generate sections on it's install, it could even generate users but I would probably check with Craft directly with this or read their license to be sure, but the methods to create such things are there in the internal API, you could take a look at the full class reference to see whats going on and whats available: http://buildwithcraft.com/classreference
With regards to template files, you can change the location of these file, see Custom template location, but I don't think you can get your plugin to do this, unless i'm mistaken.
As for theme files etc you could have a set directory structure when people install your theme and then use something like the
File class to interact with these files http://buildwithcraft.com/classreference/etc/io/File
I hope that helps you get off to a start with building on Craft