I’ve been thinking about popping up the thoughts below for some time, but have been debating whether to start a new thread, or add it in here…
My hesitancy stems both from the fact that I’m (on the one hand) not sure as to whether I’m missing some feature that could solve my problem – vs (on the other hand) whether or not this is even remotely feasible, since what I’m asking would involve such a profound overhaul of the UI/underlying functionality of how things work in DTP, so as to basically involve my asking for the pot of gold at the end of the rainbow (or monkeys riding unicorns…) 
But… nothing ventured - nothing gained… 
[b]Improved wiki-links functionality…[/b]
There is little wrong with how it’s currently possible to use the Annotation feature, to inbed links to other documents. I use this extensively. It works well to a point, but then (possibly through over-use??) it starts becoming less useful.
Case in point: I might have a lengthy pdf of say, a piece of legislation – 300 pages… Several sections of this Act, might be important to me. I might come back to it repeatedly, as I work, since at different times - for different reasons - I’m focusing on different sections.
A.)
I could create one lengthy annotation, that I constantly add to, highlighting my thoughts about each of those sections – added to over a period of time, as I keep coming back to the PDF in question.
I can use the very useful scripts, to create live-links back to specific sections of the PDF, so that using the Annotation in this manner, has me jump back and forth, only to where I need to be… One that I also use regularly can be found here: [url]QuoteHighlight&Annotate script]
With screengrabs/comments/wikilinks/paragraph selections/thoughts/ramblings etc. - the Annotation can quickly take on a life of its own, bulging into something that almost becomes as long as the original PDF [ok - not quite, but still! 
]…
B.)
I then sometimes try and tidy this up, by using korm’s (with Christian) very useful script to “explode” the RTF, into many separate RTFs that all link back… This works well in certain cases, but not in others [not at all a critique of the script - just my usage scenario] - since it requires me to be more careful with how I compose the initial RTF, in order to have the script kick in properly… [see here: [url]Explode and group a note (split & title 2)]]
Alternatively - I simply create my own wiki-links to other RTFs, using the inbuilt wiki-link functions with DTPO… This works well, to an extent - but does occasionally result in my almost spending an equal amount of time creating the links between different RTFs, as what I do in creating the comments/thoughts/information contained in those RTFs… 
C.)
Or even worse – I come back to a PDF I haven’t looked at it a while, and fail to notice it has an annotation attached [one sometimes/often(??) misses the little live-link at the top of the PDF!]… So spend time jumping through the PDF in question, trying to get to the bottom of some nagging thought you have about it – only to [5/10 minutes later], stumble across the annotated RTF, with that exact same thought (and associated comments) having been made already - 6 months ago…
D.)
Lastly, and possibly the most problematic scenario for me [not sure if this is shared by anyone else??]:–
I have a Source PDF – and I have any combination and number of the following:
(i.) a Bookends RTF that was imported, containing the reference information to that Source PDF [which also serves as a useful point to jump straight into Bookends, to the relevant citation entry];
(ii.) A RTF generated via Goodreader on my iPad, containing only the comments I made about that PDF, when annotating it inside Goodreader – see here: [url]Need some help re my Annotation workflow-DTTG<>Goodreader];
(iii.) An Annotation RTF - containing comments/thoughts about that particular PDF;
(iv.) Several(??) Annotation RTFs linked to other PDFs, that are in some manner related to the Source PDF;
(v.) A webpage downloaded into DTP - or several of them - if it’s a particularly contemporary issue, that might add background to the PDF in question [Wikipedia features prominently here]
Put simply, I have several diverse documents that I want to link in some manner to one PDF, with more being added, after the fact.
Currently, whereas I can easily insert the details of the Source PDF into these other RTFs/documents - the only way I can think of setting-up the 2-way referral (from the Source PDF back to those other RTFs), is by manually pasting their item-links into the Source PDF’s annotated RTF…?
Alternatively - I could manually drop something into the Spotlight Comments field of the Source PDF, for instance, the other RTF’s item-links…
OR – where I have the Source PDF and (for example) a Wiki article converted to PDF, I then need to create two Annotation RTFs, for the purposes of having them serve as the landing-page for the links between the two documents…
What would be amazing (like unicorn-riding monkeys):–:
Some sort of integrated wiki-link menu, possibly in the context of the customisable meta-data editing that has been requested - something that would:
1.) Allow for easy [drag and drop?] creation of links between documents, to populate a particular “field”;
2.) Invoking this option, opens either a floating window or a side-bar (similar to See-Also), where these links are displayed - and are live-clickable to open in tabs/or in a new window;
3.) That the system is robust enough to allow for multiple links to one document [and here, allow me to be 1st to say it – I don’t have a clue as to whether this is even remotely possible, given constraints(?) that might exist in OSX??]
4.) That the UI of the above, allows for easy jumping to linked documents from the original source document, and not exclusively through a separate RTF…
4a.) That the RTF Annotation concept, somehow is incorporated into the the metadata of the original PDF – or at least, to have the option to do so;
Regardless of the feasibility of the above – one thing I really would like to see, if none of my rambling is possible, is far more prominence being paid (visually) to that live-link to RTF Annotation, at the top of the PDF… Flashing disco lights for instance, so that I don’t go an re-invent the wheel when I’m deep in thought, only to stumble across the RTF after the fact, with evidence of my already having done that…
I apologise for the length of this.
TL;DR – Improved functionality wrt two-way linking for multiple wiki-links to one document.
