A slight extension to my previous topic 'polymath kerbals' :
Yes, specialised skills. Instead of just being a 'pilot', a kerbonaut can either be a plane pilot or a rocket pilot and why not both? A pilot has to be trained in both fields to fly our dear SSTO(as mentioned, I have posted this new multiproficiency idea in a different topic) which adds a nice little challenge to SSTOs and not all pilots are qualified to fly out state of the art piece of arts.
Scientists can be labrats or field researchers.
I don't have any idea for engineers yet.
Although I think having too many specialisations would be overwhelming, 2 specialisations for each skill in my opinion would be enough!