I think the multitasking screen might be tricky as well, as has been pointed out elsewhere (can't find the post right now). I don't remember the details right now but the windows are not just static screenshots of the apps, but dynamic. So when rotating the MT screen you have to switch all open apps to their other orientation. This might take a lot of resources (have no feeling for how demanding it would be, but a slow and laggy switch between orientations would be definite turn-off with an otherwise snappy device).
Also, all applications won't support both orientations (I think it would be a mistake to force them to, see below) which complicates it further. It might look a mess with windows in different orientations? Personally I think it would be a mistake to force all applications to have support for both orientations. Besides increasing the load on app developers, I am pretty sure not all applications work "well" (as in being practical, intuitive, logical, usable etc) in both orientations. But yes, there is in-built support for applications to have both orientations if I have understood it right. It's up to the developer.
Having square widgets/shortcuts etc (or rather forcing them to a grid with square slots) would solve the entire homescreen problem as far as I understand. Question is if it is worth the sacrifice. Without having used either blackberries, iphones, n97s or n900s I think I prefer the n900's homescreen system and wouldn't want to sacrifice the functionality. Also, it would mean redesigning the entire homescreen functionality and all widgets...