Too complex for us to answer....we don't know your location or ground temp. Heat loss in your house. So if your comfy in your house now then size it the same as you have. I are short on AC or Heat then upsize. Your ducting problem could be solved with booster fans at the registers.

Bigger question is what is your payback period to savings...geo is so expensive to pay someone to do...There are other methods with quicker paybacks using air source type heat pumps.

I have installed my own geo in two houses with heated floors so have some history. Good Luck...