I visited the place a couple of months ago. Having seen the old Aviodome a few times the new setup is a huge improvement with regards to space and options. There are many more possibilities in this building, in the old dome the whole collection was a bit cramped. When I was at Lelystad the place still had a bit of an 'unfinished' look, this will probably still be the case but they are working hard.
Indeed a few airframes are still stored, partly in the storage hangar, but there are also a couple of lorry loads of smaller bits still in storage at Schiphol I think. The storage hangar should be open most days, but the rear area will remain as it is for a while. In a way it's an interesting guessing game: see who can spot the most aircraft and identify them all
Some of the airframes here weren't on view in the old dome either, so there's probably plenty of work to be done on them before they're fit to go on display.
Overall the museum is definitively worth a visit. If you've got the time then I'd try to visit both the Aviodrome and the Military museum at Soesterberg. They are about an hour's driving apart and the Soesterberg museum is another quality setup.
This site has a large collection of photos taken in and around the Aviodrome, mainly focussing on the move over there. It gives an idea of the amount of work that was put in.
http://www.aviation-top-pics.com/
(look in the menu on the left for aviodrome)