Hi Bikhu,
There are at least two ways that might work towards your idea of animation in Cinema 4D.
• A pre-comp in Ae is like an “XRef” option in Cinema 4D.
• The Animation Clip system works like layers in Ae, but of course things in real 4D works a little bit more complex than in 2D (or 2.5D)
After Effects has its roots in 2D and even today it is palpable more often than not that it has this heritage. I think there is a good reason why Cineware makes some sense, and the combination of Ae C4D even much more.
To apply your idea to the workflow in Cinema 4D might have some advantages right now, but on the long run I think you might limit yourself. As everyone has his/her very own idea how things should be and the kind of work one is doing varies heavily, you might try the two options I have described above. Perhaps you will never miss a thing. I can’t really answer that.
I belive that both options (XRef and Animation Clips) have a huge potential for some areas. However, as with pre-comps it might has some side effects. You will answer that for your work better than I can do this with my limited knowledge of your workflow.
As in most parts of the industry (VFX and Motion Graphics) we are all aware that sometimes Time-Line/Layer approaches are great and sometime Node based workflows are the best. Again, it depends, and the sooner you know what works for you, the sooner you can refine it.
My best wishes