Engine idle speed
 

The goal of my mods is to eventually unload my Toyota Echo 1.5 L motor from the alternator (do the regen braking thing) the A/C (which I hardly ever use), and possibly make the water pump electric driven.

My question is the idle speed of the motor, will it change? And if so will it lower or increase? And am I going to see FE improvement when in idle?

The idle speed will remain the same. The ECU keeps a certain idle speed and adjusts the amount of fuel to stay there. You can observe this by suddenly turning on a large load when in idle (defroster, lights, etc.). The sudden load slows the engine down, but the ECU adds fuel and the rpms go back to normal.

If you take off your alternator or AC belt, then the load on the engine will be smaller, so less fuel will go into keeping it at idle speed.