http://www.quora.com/Should-I-use-a-game-engine-that-is-already-made-or-should-I-take-the-time-to-make-my-own

Notice that only one answer states you should avoid a game engine altogether. Another answer suggests a game framework, which is closer to an engine than what you're doing. Everybody else say use a game engine unless you just enjoy building game engines. A game engine will simplify a lot of your current tasks like having built-in GUI systems for things like buttons, layers for hiding/showing or activating/deactivating different objects without moving to a whole new screen, a method for quickly positioning objects on the screen, a better graphic rendering system to reduce processing power requirements, etc. Designing a tool for handling bayesian probability is just a small part of the steps to building your game. AGS isn't necessarily the engine you should be using, but you should be using a different toolset than just Java. The time spent learning an engine is lower than the time required to do this from scratch.