Actually I never used the old separate find window, and I think a find pane is (generally) the right thing. However, for the life of me I never can't seem to identify to which of my dual listers the find pane belongs, or especially if I do searches in both lister panes.
This is of course due to the current find pane's (sorry, major) design flaw consisting of the find pane spanning all listers. This doesn't make sense and obviously is only due to the fact that "find" and "synchronize" share the same pane (where with the latter the spanning of course DOES make sense, but not with the former).
Additionally, the find pane gets ridiculously wide if you use multiple monitors.
Thus, I'm absolutely convinced that the solution would be to have the find pane span ONLY the very lister it belongs to!