It has been made apparent now that there are many hardcoded limits in the game, which cannot be modded around, and are like a brick wall once you hit them. For example, here are some hardcoded limits that I have come across:
Structures and units - These cannot be changed or altered, which means that you cannot mix unit types. You cannot have a orbital defense cannon have fighters and you cannot have a fighter bay have weapons
Captial ship limit. - the limit was 5, but this has been now changed to 9 in the 1.1 BETA, which IS much better
Weapon limit - you cannot have more than 3 different weapons on a ship
Ability limit - You cannot have more than 4 abilities per unit
Star Abilities - you can only have 1 ability on a Star. Planets can have 4
Sounds - there is a max of 1100 sounds, spread across dialog, music, and effects. The cobination of these files cannot reach 1100, or the game will dump
MODELS- the 3D models, or meshes, can only have a maximum of 10 emitters for any particular weapon, engine, etc., or the game will crash.
STRING FILE - EDIT - No limit now, as far as I can tell. I have over 5780 entries so far.
I am writing this for all modders, so that they know that there are hardcoded limits which they cannot be changed or modded around at this time. I am also writing this for the developers, in hopes that they will read this and consider changing these limits so that us modders can do what we do without having to worry about hitting an invisible ceiling.
I would appreciate everyone's support in this, from both modders and gamers alike.