I've spent nearly two months going through several forums, including CreativeCOW's, to find an answer to this problem.
When we import ProRes 1440x1080 50i footage into After Effects, it's a lot less noisier than the 1920x1080 25p Animation Quicktime file we get out.
At first, it was the level problem where there was an apparent drop in level between the input and the output. We got that sorted by setting Project Settings in AE to 'REC 709' right before we export and the Legacy checkbox checked. It might be important to mention that when we go into REC 709, the footage looks awful in the AE display (gamma is way off even after we've set the Display Settings to REC 709) but the render comes out with matching levels. However, there's nothing that's fixing this awful digital noise that's pouring out. Our film is in B&W, so the noise becomes even more apparent as soon as we drop a desaturator on the Animation footage.
If there's anything anyone might have not mentioned in others' posts relating to this sort of thing, we're all ears!
I'm curious as to why you're stretching the horizontal resolution of your clips.
if they're 1440 native, are you dropping them into a 1920 wide comp?
Wouldn't it be better to keep them at 1440, using pixel aspect correction in the viewer.
Are they going back to f.c.p.? if so, keep them at 1440 with their native p.a.r., and f.c.p. will still know how to display them correctly.
Also are you working in 16 or 32 bit?
Why not render to ProRes HQ rather than Animation?