This is incredibly annoying, and it's easily my biggest gripe with Lion; I was looking forward to finally having fullscreen support in Safari, but instead I'm just using a maximised window like I always have, and that doesn't seem like it's going to change for Mountain Lion.
As I see it the problem is partly how to handle transitioning via Mission Control/Spaces, and how to do the menu bar. In the past, a full-screen app on a secondary monitor would still pull up the normal menu bar, ideally each screen should get its own menu bar (or rather, each full-screen app should get its own menu bar on the screen it's on, with secondary screens skipping things like menubar widgets, clock, etc.).
Still, even with proper Fullscreen support on multiple monitors, it still wouldn't solve cases where you want two different windows of a single app full-screened on different displays. In Quicktime 7 for example it's possible to watch two movies simultaneously on different screens. I suppose Apps could probably implement this, but it'd be a pain to do right.
On that note, has anyone tried Quicktime 7 on Mountain Lion? Support for Perian and proper full-screen support (as well as the much more precise skipping around within movies) are still years ahead of Quicktime X's backwards behaviours.
At the end of the day though, Fullscreen apps are just not a feature suitable for desktops. What we need are Fullscreen windows, which sounds similar but is functionally very different in practise.