Actually, I think the Parasyte/Item invocation thing is less complicated then it would seem. Basicly the parasyte it a part of your body, where as an equipment type is mearly a tool to use. You can feel the wants and such of the parasyte, but the equipment you have no clue to how it feels. That being said, the innocence has been shown to have it's own mind. I think that Lenalee is having her problems because she isn't feeling what the innocence feals, which is key for parasyte type invocation.
Also I think Cross already has the way out, or at least he thinks that he does. He did beat his way in, so I can see him thinking the same thing in reverse (if the access point did close). On that subject I think that the "egg" of the Ark is actually inside the new Ark... well maybe not, but it would be cool.
As far as the Kanda/Crowly thing, maybe they are in that Huge Black Slab that Cross is standing on. Now, I will probably get yelled at for this, but I kind of hope they are actually dead. Don't get me wrong, I actually enjoy the charactors a lot, but we need the series to go dark somehow and this would dampen everyone's spirits (yes, even the constantly happy Lavi).