Thanks for the additional details. Pipeline means to me from start to finish, not just authoring the elements. Hence my longer text and my caution to be not able to give anything but some general directions.
Well, as detailed in my “JET” series, where I combine practical shots and 3D, I did most of it in a 2D application, speaking of compositing.
On the end your knowledge and experience (training) will always count more than which app you use, etc. Focus on the final results!!!
There are certainly two main directions to organize it, you know what you want and those things are created. OR: everything needs to be as “last minute” in the decision pipeline as possible. This rough differentiation will guide you and determine your workflow.
There is no right or wrong, but there are of course consequences of each.
A good prepared shot will be cheaper and better than to keep things open until the end. On paper 1%, on set 10% in post 100% to express roughly a rule of thumb in cost and work. To keep things a live, e.g., 3D in during compositing slows most-likely things down close to the deadline. The more you can render already, the faster your compositing pipeline and feedback loop will be. If the green-screen key is pulled and the renderings are done, it is easy (eventually via proxies) to focus on color and details. If everything stays alive, not so much. I hope you get my drift. There are certainly other ideas about, but I hope it gives you something to consider and find your own sweet spot, as no one else can do that for you, without discussing the project like a VFX supervisor would do.
After Effects is great, but Node based compositing has so much more to offer, but the learning curve is steep compared to Ae, which is rather simple. Which brings up the point who much time you have to get this knowledge.
My advice, just take a shoot with a single actor and move it one time through the sketched out pipeline, then try another approach. You might have a personal preference and that counts as well. Or your team.
I guess these three main parameter should support your discussion process. Decision based pipeline, Knowledge based option, personal preferences.
years ago I would have added hard ware and software, but with Fusion now for free, and CPU’s fast enough and cheap, that has a minor influence, but it has one.
On the end nothing maters more than the quality you get out of it, anything else is forgotten when people become your audience, just what is really visible.
You have obviously Cinema 4D, build your set there, keep it flexible with Layers and Object Buffers.
With the sets already in 3D, you can create a Story Board with dummies of your actors in Photoshop.
While doing so, you might see already problems.
If you use Ae or Fusion is a call only you can make. Yes, learning an application is the biggest investments, not the price of the package. But free and good as in Fusion can’t be beat very easily.
All the best
Perhaps have a look at this presentation:
https://www.cineversity.com/vidplaytut/nab_2015_rewind_barton_damer