The long and short answer is that you are using the wrong tool, but since you already tried Premiere and were "overwhelmed", well, I guess that settles that. Seems to me you have locked yourself into a corner by habitually using PS for everything, no matter how awkward. It would really be easy to export all your graphics to separate files, import them in Premiere, build a prototype project and then save everything as presets. The same would be true for After Effects. In fact you could probably create a lot of stuff even natively in both programs using the titler tool or effects... Also what you describe is exactly what tools like Camtasia Studio also do automatically based on the mouse and keyboard data recorded during the session. I know it's not what you wanna hear, but it seems to me you are really using the wrong set of tools... As for solutions in PS - perhaps there's a way to get the edit points with scripting and then apply transitions automatically, but that's most likely as good as it gets...
Mylenium, thanks for commenting!
Yes, i understand that other programs than Photoshop are better. But after the next ten software tutorials i have to do, i don't know if there is any more of that work so i hesitate to invest a lot of learning time (and maybe money). Might be wrong of course.
Also i want to stress that the vector graphics i put into the videos do not have to follow the cursor. I don't need any changes to mouse paths or any concentration around mouse paths.
So my question remains - how to apply transitions in Photoshop CS6 videos quickly and not one-by-one manually?
You mention scripts, but i am not able to even try that. I did not try actions (which i would be able to use), but i just can't see that they could work here.
Thanks again and more comments are welcome.