-the tree of the file manager constantly auto-scrolls left and right (once you manage to discover the setting to actually get a tree in it)
Tree is largely surplanted by the column view mode and view splitting. I used view splitting rather than tree even in 3.5 so I guess I missed that one. Try column view mode though.
-in kate the search for text has its case sensitivity independent per file, and hidden behind something on which you must click first
this option is not hidden in the current version of kate, is still independent per file. down arrow gets you the last search term from any document however and there is a find in files command for searching in multiple documents at the same time.
-by default everything is huge and there don't fit many open window buttons in the panel
This was true of early versions of KDE is much less true now.
-it is extremely frustrating to create a launcher for a program in the taskbar. There are at least 3 systems, and all 3 are annoying, sometimes involving having to manually create a desktop file somewhere. How it should be: a single drag and drop movement
this can be done with drag and drop in the current version of KDE.