#1) True. It does not use an MVC paradigm. That's not the way it was designed, and they're not able to make it MVC w/o breaking backward compatibility with the huge ecosystem of plugins and themes that currently exist.

#2) True, and I agree. The function naming could be improved. If you don't know what the function does, look it up in the codex or the source code. The documentation could improve, too, but one of the stated goals for their next development period is improved docs.

#3) Look at the docs. Yes, the_title() writes to the page. If you want to use the title in a variable, there is get_the_title(). There are generally other functions or parameters you can do if you want it to return the value rather than writing it.

#4) False. The comments template file is comments.php.

#5) True.