It's something of a toss up. The prince has more options in terms of special rules to choose from but far fewer war gear options (unless he takes war gear as his special rule). His normal choices like shadowfields, shimmerfields, bikes, and void sabres are all pretty useful though. While the +1 strength, pyschic option, and reckless abandon make for a more flexible character than his limited arsenal would seem to allow.
The Autarch is basically the opposite. He's only got 1 army wide special ability, but it's very useful. His war gear is where his customization comes in, and even stock he's better with haywire grenades and a 3+/4++ (while being 5 points cheaper). From there, you can kit him out to be anything from a JSJ heavy weapons platform, to a lance wielding biker, to a fearless jet-pack suicide bomber.
To be fair, it's the prince's formation that grants further bonuses like hate bringer or sky burners. Although the autarch has no formations built around him with sweeping rules, craftworlders do get some pretty decent formation bonuses which still stack with his reserve bonus. So I don't think it's as simple as "princes gives this, autarch doesn't". There are also some down sides to princes and their formation, although most people will always avoid them, this just means we're limiting our choices.
Overall I'd give the advantage to the autarch. This advantage shrinks though depending on how large a game you are playing, as the army wide rules princes bring effect more and more units.