@ jprint714 I’ve often shared your dilemma. Long before the appearance of the Annotation template, I was in the habit of creating a rich text note linked to a referenced document, to hold notes about it.
Sometimes I found it useful to create separate “spinoff” notes that went into more detail about an item, and/or might refer to other notes or references. It was possible to do this, although a bit of extra work is entailed to enter appropriate links, as well as to indicate in the primary note a searchable “cue” that such additional notes exist and links to them. A bit of grunt work, but doable.
The Annotation template provided automation assistance in creation of the principal note document and linking to the referenced document, as well as a link to the Annotation note from the referenced document.
The Annotation template didn’t change my habit of sometimes spinning off additional notes linked manually to and from the Annotation note and possibly to other notes and references as well. That still involves some grunt work.
I haven’t heavily used Frederiko’s annotation script yet, but see it as a possible way in my workflows to reduce some grunt work, when used as a means to “explode” individual items outside the Annotation note. There are number of ways in which one can searchably indicate the existence of such additional annotation notes, some of which could be customized in the script. Still other possibilities will probably appear in the next generation of DEVONthink.
@ Nhaps: I mentioned J. R. Partington as an exemplar academic researcher because (although he did not have the benefit of computer assistance) he was a prolific writer and his influence as a teacher and researcher has long outlasted him. He was of course a genius, fluent in many languages and a workaholic. Above all, he could think “outside the box” and illuminate topics from new perspectives. His accomplishments used the tools available to him: wide-ranging knowledge, print, pen and paper and a remarkable intelligence.
DEVONthink has a niche market. Although there are many thousands of Mac owners who have substantial information collections and feel a need to use software for that purpose (and we do well among such users), millions of Mac owners do not feel that need (however we may wish they did).
DEVONthink is already a complex database system, especially in the Pro and Pro Office editions. It provides a lot of tools and commands. That makes it useful to many people, some of whom accomplish extraordinary things, and some of whom, like korm and Frederiko (to mention only two of many), provide assistance to other users by developing scripts that enhance DEVONthink, or provide tips on how DEVONthink meets specialized needs…
Ironically, it is the complexity–in terms of the number of tools, commands and scripting capability–that almost guarantees that DEVONthink will not become a mass market product. Many people will download a trial copy, take a look at the user manual and decide the learning curve is too high for them. I try to get them to start simply, to satisfy a simple need and then experiment to see what other features might be useful, a stage at a time.
QDA software is an even smaller niche market, and has its own niches. Much QDA software is hardwired for cases in which a researcher tightly controls the environment and vocabulary to be analyzed, such as responses in a forum group conducted by an advertising or marketing agency, or a psychology experiment. That’s not a direction in which DEVONthink is likely to go. But we’ve received comments from researchers who use both DEVONthink and specialized QDA software.
The next generation of DEVONthink will in some respects appear simpler, yet provide still more power. After more than 12 years of experience and the attention of the developers to user suggestions, I expect that it will please current users and am hopeful that it will attract a larger audience. I’ve been a heavy user of DEVONthink myself, since 2002.
Having dropped a hint that there’s a next generation coming along, it’s our policy not to predict a release date. To borrow from an old commercial, no wine before its time. 
