IngotAPI is similar to Bukkit's API to try to smooth the transition for developers moving from Bukkit. After release, the API will be considered stable and have very little changes, allowing developers to safely build against it.
For newer developers, the IngotAPI is the best option to start with. Everything in the API is done via function calls. Those of you who are more daring and want to mess with the system itself without being limited by the API, you can import the IngotEngine into your project rather than the IngotAPI. All variables in the IngotEngine are public, so hack away to your heart's content :) Just, if you break something, know it's most likely your fault :P