2007 lexus is230 left in neutral overnight and run battery down. tried to charge up battery,disconnected battery over night,tried new battery in remote. battery is at 12.2 but will not start.

 

What does it do?
New battery has only 12.2v?
Not good. 12.8 - 12.9 fully charged at room temp after sitting off charger are good values for a healthy battery.
What does it drop to when cranking? Does it crank (spin the engine over)?

 

I assume you moved the shifter back into "PARK" and were hitting the brake pedal while attempting to start it?