I don't know what problems you are talking about, all you need to do is plug your Kindle Paperwhite in (if/when you get one, that is) and send books to device as normal.
No changing formats is necessary. Unless you have books that are not in the Kindle format, in which case calibre will convert it for you automatically. (It may prompt you first, just click yes.)
Anything books that worked on the Kindle 2 will work on the Paperwhite as well. Unless you are using complex options and plugins to do weird things, etcetera, which it doesn't sound like you are. That is where the confusing issues come in, but fortunately, the only people who have to worry about that are the ones who already know how to do it.
And possibly enjoy doing it too.
Go for it!
The newest Kindles have some nice features, especially the frontlit screen on the Paperwhite. I'd say that's a good reason right there.