I've just been poking about with this myself, and here's what I think may be going on in the Apple engineers' heads:
- iWork apps for iOS don't support all of the same features as the desktop apps - cell comments in Numbers is a simple example, but there are others, like some complex formulae
- When you upload a document from the desktop environment, iCloud.com/xxx converts it to a format usable by the iOS app - and it warns you when certain feature are about to get stripped. In my case when I uploaded a Numbers '09 doc from my MBP, it warned me that my comments were being removed, as were references to two fonts that weren't available, and some other (unnamed) complex formulae
- Once the docs are in iCloud, the iOS apps (which support more-or-less the same feature sets as each other) can seamlessly share without any problem, but if you were to download back to the desktop, you won't have all those fancy features you originally set up.
- Therefore, 'they' don't want you to be piqued because all of sudden your comments and formulae are gone on your desktop version.
Now, I'm not saying this is a Good Situation - in fact, Dataviz seems to have struggled - and more or less overcome - the same problem with DocumentsToGo (the bit about allowing a stripped-down editor to update a document without removing the richer features). It would be good to see Apple implement whatever conversion algorithms Dataviz are using, and then expand to close this rather unfortunate usability gap.
As it is though, iCloud is (almost) great for those who are leaving the desktop behind entirely. And I sympathise. With iOS5 + iPhone 4S + iPad 2, I'm almost there myself.
[And this is essentially what Sjazbec is pointout, above - cheers to you, Sjazbec.]