Compressor 3.5.3 cannot output an H.264 mp4, so you must be using an actual mpeg4 codec setting, which typically isn’t the norm. H.264 is the go to codec for uploading to web. File size is largely dependent on bitrate, so yes your MP4 is smaller, but you also say you’re getting pixelation and artifacts, meaning your bitrate is too low. You’re trying to encode a 90 minute 1080 video, it’s going to be a large file. Creating a file with a bitrate of 8,000kbps is still going to give you a 5.5GB file. You could scale the video down to 1280×720, encode at 4500kbps and still get a 3.13 GB file. Then Vimeo is going to re-encode your video. You typically want to give them a high bitrate file since they re-encode.
Encoding speed all depends on your hardware specs, but I really don’t think it should take your system 48 hours.
@ericstrand11