Upgrade ship weapons to as high a particle beam as you can. Buy and use ship parts. upgrade your shields.

He stops handing them out for a while, but does restart eventually.

Also if you choose to do a multi NG+ run, any temple powers you do not pick up are available in a later one. What I mean is, if on your first NG+ game you only upgrade 3 powers to lvl 2, the next run will (eventually) let you get ALL powers to lvl 3.