Technically, there is no particular codec that's better or worse. For our footage shop, we store everything in Prores 4444 with premult alpha, or Prores 422 when the content doesn't have alpha. We then batch out to DXV and h264 via Compressor.From a technical standpoint, does DNxHD, ProRes, Cineform or another intermediary codec stand out as ideal for the step between AE/AME and mpeg (or whatever is best for batch?
On PC, I'd probably go with PNG sequences via AME.