Hopefully the WebApp Pool will be about as easy to use as Fantastico, and will offer more flexibility in configuration than Fantastico. Over on SMF, they recommend against using a Fantastico installation, because it 1) installs all language packs, whether you want them or not, and 2) does funny things with UTF-8 encoding that inevitably leads to problems with later upgrades. (Speaking of SMF, does Lunarpages have a redistribution license with them, so SMF can legally be offered?)
I haven't heard anything official, but it appears that cPanel will be going away, at least as a free feature. It costs $$ to offer cPanel (or Fantastico separately), and I would presume that LP wants to cut costs as much as possible. This motive would be in addition to their desire to streamline administration. cPanel also has some clunky function with things like handling subdomains and add-on domains, and updating .htaccess in other than the root directory. Hopefully those are being addressed in LPCP. Anyway, once they have LPCP up and running smoothly, it would not make sense to stay on cPanel for the older servers (except where users are willing to pay an extra fee). I would assume that eventually even existing cPanel accounts will be moved over if users don't want to pay an extra fee (or at least, don't rule out that possibility).