Change the way Skynet works, from ban delays, to VPN probability, to the color scheme. Skynet is yours.
Each heuristic is housed in its own Jar file, which can be dynamically loaded, unloaded, enabled, and disabled on the fly. This means you can write your own heuristics, or easily port existing ones.
Is the config not enough? Skynet's addon system has its own event handler, unique to the anti-cheat's mechanics. Even adding your own events is a breeze.