I was married to a musician, a guitarist, so for the months of our lives each year that were spent on the road of course he traveled with his instruments. In your case I'd certainly not take your favorite. Resign yourself to paying extra at times or even checking it, so good case required. Another option would be to use a replaceable instrument so if the worst happened you could buy another.

Our worst nightmare occurred in NYC when a taxi drove off with irreplaceable instruments, scores and uniforms. Never get out of a cab anywhere before the driver if there are things in the trunk.

I was just looking into this recently.
There are a number of guitar companies that make travel specific guitars that either try to cut down size or weight or a combination of the two.

This site has some interesting options: http://www.voyageairguitar.com/

And this guitar has had some great reviews : http://www.amazon.co.uk/Martin-Backpacker-Guitar/dp/B000Q85NQ2