I have personally brainstormed a mind flayer mod but have 0 modding experience hence why it never happened so Ill just lift off the stuff I thought about feel free to do or not do as many as you want

• Mind flayer portrait, namelist and shipset
  
• Access to Psionics through either enabling a modified vanilla route or a mind flayer unique path
  
• Mind Flayer unique army (plus an ilithid Dragon as an endgame army?)
  
• Mind Thrall Colossus Weapon
  
• Unique Mind Flayer ship weapons (i.e. Psychic lasers and tentacles)
  
• Necrophage style Vassalisation (Where you get pops from a vassal state periodically)
  
• A custom origin where you get a mega structure version of a super Elder Brain in your starting system being the physical representation of your leader you upgrade throughout the game gaining larger and larger empire buffs.