If I were the coaches for the Chargers trying to decide between Stick and Jones, I would be looking at these things:
a) How did Stick do in the games and in the practices compared to how Jones was doing in his first year (first 3-4 months).
b) Are the mistakes of the two QBs, mistakes that are fixable? Or are they just because of a lack of ability and talent?
c) When they played at their best, how good were they - in execution, in getting the teammates to work as a unit, in inspiring confidence, etc. In other words, what is their upside potential, all things considered. If one has an upside potential of 10 (the best) and the other an 8, then the '10' is the better choice.
When one is comparing Stick with Jones, one is comparing apples to oranges - one who has had only a few months to adjust to a new environment, learn the plays, and so on, compared to one who has had about 30 months (10 times more time).
On these things, I think Stick does well. Employers often look for shortsighted things when making a hire, like how much did this person make before, what do his or her references say about him or her, are they from the area -- because many or most do not know what kinds of questions to ask or what kinds of preliminary exercises to give them in order to find and see the raw talent and ability, the stuff that shows their upside (that is, how good they really can potentially be).