I’ve spent a couple years looking at Agama vs. Pali parallels, although not as much as I would like since most of my time is spent translating Agamas.
One thing that’s clear to me is that it’s a complex situation that exists in the extant canons. It’s not really a matter of whether we should be studying whole suttas or the repetitive bits that are scattered throughout. Both methods have their place. Clearly, there were distinct suttas that arose that existed in multiple canons in different versions. The different versions seem to have naturally diverged more or less from each other, and occasionally there appears to be conscious sectarian editing on some of the sticking points of doctrine. So, there’s a place for selecting a given sutta and attempting to trace its development using the various parallels that exist.
On the other hand, there are these formulaic tracts that exist in Agamas and Nikayas that span many different texts. It is important to study them as well. There are a couple different things this can reveal. The first thing I think most scholars of Pali have already realized, which is that they can reveal the historical strata inside a canon since the formulaic material is evidence of consistency editing. Plus, sometimes the formulas grew in size and appeared in other genres of Buddhist literature. An example I can think of is the formula describing arhats that includes “laid down the heavy burden, won their own reward” etc. This formula became standard in the introductions of Mahayana sutras, and it can also be found in some Pali suttas and Agamas, too.
Another issue that I’ve noticed is that the equivalent formulas in one canon and another can vary quite a bit sometimes, which also tells us the exact formulas sometimes were “carved in stone” within individual traditions. An example of this is the long, standardized tract that lays out the training that culminates in liberation found in DN, MN, DA, and MA. There are three versions of it that I’ve seen so far. The variations aren’t earthshaking, such as the number of precepts listed out, but it does show that it’s a semi-sectarian formula. Another example of this are those controversial metaphors for pleasure filling the body associated with the jhanas/dhyanas in some traditions (Theravada and Dharmaguptaka) and not in others (Sarvastivada). So, again, one wonders what happened there, historically speaking, when we look closely at the parallels.
All in all, I agree with @sujato that we have a large amount of basic work to do still. The Agamas need to be translated and studied more systematically, and not all the parallels have been documented and studied in English, either. It’s good that we’ve made a solid start in the past couple decades, hopefully the momentum will sustain itself. The real heavy lifting is to study the different parallel canons more systematically because of the sheer amount of material involved. But we need solid translations to help facilitate that. Scholars shouldn’t need to be ancient language polyglots to access the parallels they want to read.