You're obviously very misinformed or your information is out of date or something.
1) Yes, it copies things into your Rails directory. Know how to fix that little upgrade problem? rake rails:update. Done. They made a task to do exactly what you describe.
2) There are plugins available that do all the things you describe, but the Rails framework is meant to be a very slim platform to build applications on. If you want all the bells and whistles, look up things like ActiveScaffold, Magic Models, etc. The point of Rails isn't to make an application for you like Joomla or something; it's a framework/platform to build things like Joomla on top of.
3) Again, plugins. It isn't Rails job to generate your HTML designs for you.
4) It's as close to MVC as you're going to get on the web. It IS MVC in a loose design pattern sense, but of course I'm not a purist so who cares.
5) You don't have to use mod_rewrite. Rails has extremely rich routing. You can make any URL point to any controller, action, and even provide custom parameters to that action dependent on the URL. I don't think Rails has used mod_rewrite in something like 3 years. Even further, most heavy duty deploys of Rails these days use nginx, not Apache or Lighty as you describe.
It seems that your opinions are based on an old version of Rails or something. So, I adjure you to go check out the new version. It's matured a lot in the past 1.5-2 years.