A list of some things I'd like to see for modding so that the devs can tell me I have my head in the clouds:
Different 'armor' types for shields and hull.
Ability to define some currently harcoded elements such as armortypes and other elements.
Ability to define firing angles (And stats?) for each weapon point.
Make it so Boolean modifiers can be based on ability/research level instead of just "yes/no"
Make it so research and abilities can have a manual 'target' list by entity file names as well as gravity well types, etc.
Make it so that each spawnable entity can have a max spawned limit.
Make it so that the number of a certain strikecraft type a ship can have can be limited.
Give each movable entity a 'canPhaseJump TRUE/FALSE' flag along with corresponding research/buff to change.
Make it so buff types and research are more versatile. Example: Instead of 'StealAntimatter', just 'Steal' and definable of what to steal.
Give each ability and research a 'ShareWithAlly TRUE/FALSE' flag as well as a corresponding research/buff to change.
Make it so research/abilties/bufftypes can have other prerequisites such as 'x of a certain entity' or 'hasPeaceTreaty with this player'
Make many, many more variable get research/bufftypes. Cost to buy capital ship level, etc.