Hi
Yes, the Wubi is sitting on top of Windows systems rather than being "on bare metal" so it's never going to be quite as good as the system it's sitting on top of.
Hmmm, i think it is a lot closer to bare-metal than it would be if installed on a virtual machine inside Windows = i think it's more like the Wine approach but it still relies on some of the flakiest bits about Windows, such as their boot-loader, registry, and Ntfs partition (thankfully (at least hopefully) not Fat32 or other Fat).
The advantages are
1. it gives you a fully working Gnu&Linux so you have easy access to all those OpenSource programs.
2. it helps you familiarise yourself with the different system to help you migrate without taking the "slash and burn" approach that people so often take (which leads them to disliking the system they are not familiar with because they can't find where things are and then blame the system for not having them even though they probably do exist or are done in a different way)
3. it's fully compatible with other Ubuntu machines (and therefore all other desktop Gnu&Linuxes.
The next step after getting familiar with the Wubi would be a dual-boot and that would get it on bare-metal. The dual-boot gives a different menu just after you start-up your machine so that you can still choose whether to boot into Windows or Ubuntu that particular time. To slow it down even more it might be good to keep your Wubi for a while because there are probably config files and data that you want to copy over to your new system. Plus you probably want to try to copy roughly the same visual set-up and additional programs or ones you've swapped out too.
Regards from
Tom