I'm using Lion with multiple monitors, too, and have been annoyed by this. But the company that sells https://www.apple.com/displays/ definitely didn't do this to intentionally hurt users with multiple monitors.
My assumption is that, because of the dramatic changes to the desktop workflow in Lion, they needed to cut some features to meet summer deadline. Since relatively few users need multiple monitors, that's one area where they skimped.
We'll probably see some sanity restored in a minor update to the OS.
I don't think we'll see any sanity return to this BTW. The very foundation of Full Screen is made in such a way to make it conceptually difficult to fix. All these problems stem from the decision that full screen should ALSO throw you into another new space, which makes it incompatible with the old workflows of having other apps running on the other screen.
It was such a silly decision (to support "swiping" I guess?) Full screen already existed before, all they should have done is update the iLife/iWork apps to support the old full screen and encouraged developers to do the same. Instead they over engineered this complex system of spaces (a feature that only PRO users are used to BTW) and broke old features. I really don't understand it.
Be patient; I'm sure they'll fix it soon.
Which is very weird considering their Thunderbolt monitor is specifically marketed for use with their laptops, and for chainability (so not just 2 monitors but at least 3).
Because they fudged support in the initial release of Lion? Get real. If you're so effected by it, downgrade until there's an update that fixes it. But don't assume that the workstation of choice among graphic artists is going to completely drop multi-monitor support just because it isn't exactly how you want it right at release.