Depends on your reasons for doing so. If you need more bootspace Skoda wins hands down. If you are doing it for interior space then it's a much closer call. Both cars do well in customer satisfaction and relability surveys. If you are just changing for the sake of it I'd consider going for and Octavia diesel as resale will be a lot better than 1.4 petrol. Driving experience would be much better also as it's a heavy car for 75bhp petrol to pull around.
A lot of people will say your mad to change such a new car but a lot more are exactly like you and change every 2 to 3 years.
What I would do is ring a few mazda dealers pretending to be trading in a 04 Octavia with the same miles and engine as your own Mazda 3 for a brand new 3 to see what sort of money they would give for a second hand octavia. Give you an idea of how resale would be.