Pocket PC Thoughts has posted an article that shows how installing software on your Pocket PC device will differ under Windows Mobile 5.0. Aside from a new process, you will also not be able to install programs to RAM, everything will go in the Flash ROM or on storage cards.
Screenshots demonstrate the complete installation process. The process is much more intuitive but could still be more user-friendly (I’m thinking of the security warnings specifically). At least we’re moving in the right direction.