If you're talking Incubus vs Python in a fight and even skill assumed, the Incubus wins every time if the Python refuses or fails to disengage. You just won't land enough missiles in succession 95% of the time to keep the Incubus weak enough to kill after the reload. The Incubus on the other hand can not only provide strong damage to shields, it does so very quickly and at a good range if your piloting skills are up to it.

Overall I'd say the Python is better, as small rails are the only anti Shield AV in the game (because lolplasma cannon), and Pythons are significantly more agile. Afterburner Pythons may be more squishy but they are a pain to hit. Without an AB they're still quick enough to disengage in a reasonable amount of time.

Most importantly though: Small Missiles. Once shield vehicles are gone from a match or at a minimum, the rail Incubus is essentially worthless and needs to be swapped to a missile fit to harass infantry and armor. The Python never needs to make that switch because Python Missiles can even punch through unhardened shield vehicles without much trouble at all.