The main problem, as previously alluded to, is that using related manga links for doujinshi doesn't scale well.
For a sense of scale, over on Dynasty Reader, there are over 2300 Touhou doujinshi and over 400 Puella Magi Madoka Magica doujinshi. Although most likely only a
tinysubset of that will ever be reuploaded here, that will still be a pretty significant number. (For more scale:
Comiket 92 fandom distribution statistics.) For just a taste of how unwieldly this can become, see the related manga section for the
Haruhi manga. Already getting a bit long there. ? For this reason, I think there is value in treating doujinshi as a special case.
It seems that as of now, most of the doujinshi already uploaded do not have a relation back to their parent work, which is good for now, because adding these relations for every doujinshi would just make the description sections on the source works just absurdly long. Many of the doujinshi uploaded here seem to follow a naming convention of "<fandom name> - <doujinshi name> (Doujinshi)" (not sure if this is documented anywhere), so it makes searching for doujinshi fairly simple, at least. But it's not perfect, because stray works from other series may get mixed in, and some uploads don't follow this naming convention.
So yeah, having doujin association with series would be a neat feature.
But I can see some tripping points. For example, series such Touhou and Kantai don't have an obvious central "start here" manga entry since the primary source material is in a different medium (
sorry, no obvious volume 1). One possible solution may be to use the placeholder manga page solution that has been brought up before, but that seems sort of hack-ish. It would be fairly simple to implement, though.
Just some of my thoughts.