One of the main problems with AIM, and something I see hang many people up because they don't notice them, is that popup dialogs can be hidden behind other windows. This can be asking to initiate a manual install, turn off the default traffic file, install a traffic file, etc. It would be in AIG and every user's interest to have these popup dialogs set to always on top.
Since they're required for AIM to continue, being hidden behind another window may make it look like the program is stalled. AIM can take a long time to load, as can installing flightplans. Because of this, users may opt to continue browsing while this is going on further complicating the issue. A popup that is hidden will not alert a user that attention is needed. Since they require input to continue, the standard should be always on top.