How to maximise the use of the code during mod development (For instance I want Alpha 1 to be a well-defined and fleshed-out character just like Blue Planet and Transcend before it)?
That is not a matter of the engine you're using. All the sexps in the world will not make a character compelling. The campaigns you mentioned make their characters interesting through their writing, not through the tech used.
Creating good characters and creating good missions are very different challenges.
The question you've asked is fundamentally impossible to answer, as it is far too broad.