quicktime pro won't copy paste

I just moved from 10.6.8 up to 10.11.4 and I too was no longer able to select my in/out of a mov in QuickTIme Pro 7.6.6 and copy to clip board into a new untitled video.

I just checked my system and the QT 7 Pro copy-past routines are still functional as long as the software (QT 7 embed, QT 7 player GUI, and video file) are not corrupted and the data contained in the file is edit compatible with QT 7. Your inability to set in/out points suggests that you have some sort of corruption and/or the data you are trying to edit is not edit compatible with QT 7 Pro. E.g., if I edit (copy/paste a segment of) an M4V file containing H.264, AAC, AC3, and Text (Chapter) tracks, I can set in/out points normally but attempts to copy/paste the segment will fail because the AC3 data track is not edit compatible with QT 7 Pro. On the other hand, If I delete the AC3 track, the remaining data tracks can be segmented, trimmed (if desired), copied, and pasted to a new player window without issue.

What the (f)Heck happend in that upgrade?

Actually, a number of things have happened. Apple is in the process of completely re-writing QuickTime. (Note: not upgrading but totally re-developing the software.) Pundits have estimated this process of evolution would take up to a decade to complete. Mac OS X v10.6 through v10.8 contained a single embed that was able to "switch" between QT X and QT 7 support routines. However, beginning with Mac OS X v10.9, this was changed to the use of independent embeds in support of the two different versions of QuickTime. In preparation for this embed division and the limitations it placed on the support of various codecs, Apple unconditionally turned off the active use of "legacy" codecs with the release of Mac OS X v10.7 making users turn back on those "legacy" codecs they wished to continue to use with the QT 7 until such time as its demise. (At this point "passive" use of the codecs is still enabled for QT 7 playback, as well as, QT X/7 natively supported conversions. A re-working of the core audio support was also initiated under Mac OS X v10.7 which was completed under v10.8 and was probably also in support of this QT support transition. With the termination of QT 7 "Pro" sales, I suspect Apple is likely positioning itself for the final demise of QT 7 support under a near-future Mac OS upgrade.

Trim to Selection will need to work, but now that ruins the workflow I've been using for the last 15 years since FCP 1.0

As already indicated, this function continues to be supported, albeit possibly limited by the codecs you are using. Apple, like most video purveyors, is in the process of transitioning from the use of a wide range of older codecs having limited specialized use to a small number of modern codecs having a wide range of uses.