My advice would be to use two seperate programs here.
First I would recommend JDownloader to download the actual videos
JDownloader is a free, open source, download management tool that supports downloading videos from Youtube, as well as from many other sites. JDownloader is licensed under GPL and is available on Linux, Windows, and OS X.
Some features of JDownloader include
- Download multiple files at once
- Pause and resume downloads
- Download playlists
- Broad website support
Next I would recommend Handbrake for the actual file conversion (transcoding). Handbrake is a free, open source, all-in-one transcode tool available on Linux, Windows, and OS X.
Handbrake's most notable features include
- Built-in device presets
- Broad codec support
- Batch conversions and conversion queue
- Subtitle and chapter support
The main reason I'd recommend Handbrake is for its built-in presets. Among the ones selectable, there are transcode presets for
- iPhone & iPod touch
- AppleTV 2
- AppleTV 3
- Android Tablet
After downloading a Youtube video with JDownloader, you would simply select the iPod preset in Handbrake, start the transcode, and then be finished with it once the conversion is complete.
Source on the first half of my post: YouTube downloader for Ubuntu