I finished a playthrough with the Griffonian Empire (Archon route). I encoutered the following bugs or oddities:

• The armour developers ("Greifswagen" and "Acturien Automobile") do not have their listed effects. They are not displayed when reseraching the Techs and don't occur in practice.
  
• The deeper focuses in the "Our Changeling Friends" branch (e.g. "Joint Industrial Exchange Program" and "Joint Technological R&D department") are quite useless because Chrysalis recalls the attaché quite soon afterwards, removing the bonus. If they are to be honey traps to sink focus days, fine enough. But if they are not intended that way, 3% reserach speed isn't that good for a focus with lots of prerequisites
  
• The Kingdom of Wingbardy is missing the "or later than 1.1.1012" bit for its "Fight the Empire" foci.
  
• "Reward the Faithful" is too random (I got to integrate the harmonists, but the supremacists with the good relations went rouge. )
  
• Naval developers for the Griffonian empire need an adjustment pass (the bonuses are all over the place).
  
• Same for the small arms - in addition they seem to be broken.
  
• Romau is odd. It isn't possible to integrate it by focus or decision while Erion is in power. WAD? In general, integrating vassals outside of the foci provided is clunky. Or playing with the vassals (e.g. the Hellquill order), as the Empire lacks interaction there.

In general, it was a good bit of fun.

Edit: In addition, the "Operation Paperclip" bonuses get a bit long despite not being applicable, though I guess that is a problem of another mod. Maybe introduce a decision to discard those?