Well, as it the first beta, perhaps things going wrong will be corrected, but here's a list of what it should get imperatively
1°) past version of Theme Manager included some more applications such as Winamp, ObjectDock, CursorXP, Stardock Widgets and so on (don't remind exactly the correct list). Though some suite already builted have these applications in, and though the new theme Manager version should get at least the same applications in.
2°) past version didn't managed correctly ObjectDocks themes. The new version should managed ObjectDock within the .ini files of objectdock themes i think (wherever are stored these files on disk and not only in C:\Documents and Settings\All Users\Documents\Stardock as you may want to ... )
3°) All Stardocks skinning applications should be added in the default applications list
4°) it would be nice to let user add some none pre-defined applications such as rainlendar, xion and others
5°) above all it would be imperative to have the options to edit an existing suite builded with Theme Manager (and not to have it to delete and rebuild from scratch like it was with past version) AND themes from MyColors
6°) for this fisrt version i think that things are confusing between elements for buiding a theme/suite and separated elements