Yeah, that drone and transport idea is probably overcomplicating things. A blend of simple mechanics and new ideas is good for a game, adding that sort of complication would probably distract from the main focus: the hypno and TF, and the management aspect.
One thing I hope you can implement in the game is a gallery of some sort. One issue with a lot of these real-time TF games is that you don't really get to appreciate the TFs when you're actually doing the fighting, or you risk getting distracted.
I love that idea of the normal vs hypno gun! Probably the hypno gun would be worse in some way, either less accurate, or takes more hits to defeat a ship.
I'm definitely looking forward to seeing the upgrades, although I feel like you might want to start the ship off with a lower fire rate/projectile number per shot, so it can get upgraded more later.
Also, I had an interesting idea: What if, when you captured people, each area you assigned a person to had a sort of "representative" who would slowly TF as you added more prisoners to that section of the ship. That way you wouldn't have to make art for each prisoner, but could still get the experience of TFing them.