A lot of distros shifted back to lilo because grub didn't (and I believe still does not) support large inodes on ext3 filesystems and it doesn't support ext4 at all. grub2 is supposed to fix that. In the meanwhile lilo is still the safest choice.
ntp being in extra instead of installed by default reflects the fact that this is a desktop-oriented distro. I don't see why pulling something out of extra is an issue in any case.
You don't need to modprobe fuse manually. If you go into the Services section of vasm or vasmCC you can just check the box next to fuse and it will be started immediately and at all future boots. VL has a philosophy of starting only what's absolutely needed rather than starting everything and the kitchen sink as (X)Ubuntu does. That's better in terms of both security and speed. Of course, if you need something not started by default you have to turn it on
So... in short your gripes are about decisions that were made consciously by the developers, not about bugs. I understand that you might have made different decisions and might have had a different design philosophy. The VL developers have an excellent history of listening to community input. Having said that I don't think any of the things you listed are likely to change. I certainly wouldn't want them to.
In any case, welcome to VL. I think you'll be hard pressed to find a friendlier or more helpful community.