Some say ProCoder {no longer Canopus) is better for long movies over 2 hours.
I use the Adobe Media Encoder mainly because Procoder is not compatible with CS3 and the Adobe thing works great.
It is slow because the default settings include 2 pass VBR and a quality level of 5.
2 pass VBr is great for movies over 90 minutes that have a good mix of motion (including camera panning) and very low motion scenes. The first pass analyzes the video for this and then takes your average bitrate, catalogs where more bits are needed and were less would be just fine.
You need to calculate your average VIDEO to fit your movie on the disc. Your max VIDEO bitrate can be as high 8 mBps. Many of us have found that combined bitrate (VIDEO and Encore encoded AUDIO as Dolby) over 8.2 mbps can cause some DVD players to choke and studder.
Encore and Premiere have the same encoder except for audio and Encore will encode the Elementary Audio stream that Premiere created as Dolby. This saver exporting from Preiere as an .avi file.
Regarding studdering, I have found that the media is often the culprit, although some players just dont like recorded DVD as opposed to replicated/
Keep your Video bitrate to below 8mbps in all cases. Encore will add .2 mbps for the audio.