The USB dongle enables installation of unsigned homebrew software - As far as I understand it, the dongle itself has absolutely nothing to do filesystem limitations.
It is the SOFTWARE that you install with it that has limitations on it - be it limitations with the software written, or be it with the access / abilities afforded to it by the PS3 Hypervisor.
It is quite possible that in the coming weeks/months/years homebrew developers will provide software that allows for Ext2/Ext3/NTFS or any other variation of file system (Assuming this is allowed by any remaining restrictions that the Hypervisor enforces).
PS1/PS2 compatibility - If you can't currently play PS1 or PS2 games - then you're not going to be able to with the PSJB until such time as a dev writes homebrew that allows you to.
If you CAN play PS1/PS2 games (i.e. have a FAT console with 4 USB) they you will still be able to - Not sure if the backup manage that is currently available will allow you to backup those games - but i'm sure there will be a solution for those with 4USB
NTFS - yeah well it might be nice (ext2/ext3 wld be better tho! IMHO), but even if there isn't any way to read/write NTFS filesystem due to hypervisor, I wouldn't think it will be long before someone writes a new backup manager that allows for split files (e.g. File.001, File.002) which would be a very quick and easy solution to the 4gb limit.
I'm looking forward to the following:-
1. Cheap clones
2. Confirmation that Sony detection can be bypassed
3. A huge barrage of homebrew, including better backup managers, VNC client/servers, Homebrew games etc etc etc