Personally, it's not worth the risk to put a 48v Nitro battery into a 36v NEO bike for the reasons Ravi stated. Go with a 12ah battery, unless you need extra torque and speed. If you want to put a 48v Nitro battery in a NEO just remember you know own a "kit" bike w/o a warranty. For some that's fine, but for most it's too much risk. Take that from someone who has been modding motorcycles, cars and other toys for over 30 years. It's a heap of fun, but you do so often with considerable risk ($$$ and safety). Just because something appears to work, doesn't mean it will stand the test of time.
What I have to often remind folks is that we are talking about bicycles here. If you can't get up a hill w/o more effort than whats needed on one of our bikes, it might be time for a motorcycle or scooter. Having measured a 730w continuous output at full boost on our "350w" motor, I'd say by most folks standards, that's pretty decent. Maybe that's why I have outclimbed a Specialized Turbo, Lapierre Bosch mid-drive mountain bike, Currie E3 Peak, and Stromer Elite on our 650b Jumper and with more comfort. Anyway, everyone has to find what works best for them.
Will technology improve, absolutely! Will battery capacity and motor efficiency also improve, certainly. When that happens I hope to be the first in line. In the meanwhile, there are some great choices our there, so find (or build) the best bike for you...and enjoy the ride seeing as today is all we have!
Peace.