Hey Antoine, there are tons of apps; that as far as I know you will not be able to run through a web app without giving it control to local APIs(which would defeat the whole purpose of sandoxing)
Things like radio control apps, volume hacks, etc. Anything that would require access to hardware API's you just won't get.
Also; I'm not aware of this being spoke of or resolved; what happens when you go offline? will you lose connectivity to all your apps? Does this built in browser use something along the lines of Google's Gears? Sorry if I didn't catch the answer to this one.
I may be asking too much, but I subscribe to Make mags motto.. "If you can't open it, you don't own it." Or something like that.
What I'm really wishing for is an larger version of the IPhone that is open and not connected to a wireless carrier.
Maybe the next IPod will be what I'm looking for.