Honestly, it seems like the way to go to have a very moddable game is a language that's easily decompiled and modified at runtime like Java or C# (or just JVM and .NET CLR if you prefer).

When they do internal modifications, but also have modders in mind, you get to have an amazing modding API basically "for free".

The only thing you need to have a very modded game is a large enough user base. A little bit of binary patching and dll injection never stopped a dedicated modder.