The way I see it
What Ra has over Isis
Empowering Priests - This definately outweighs the -10% tech cost to me, since you can empower all your resource points, you will earn more than you would save(maybe not too much, but I do believe you will have more resources in the long run), and while playing isis, I kind of feel forced to keep the pharoah at home empowering rather than on the battlefield kicking in MU's heads because he is the only one who can empower, no problem with that with Ra.
Stronger Camels and Chariots - if the match goes on into heroic, this bonus really takes on to its own, as both units are very useful on the battlefield.
Cheaper monuments and they are stronger - any bit of money saved helps, and monuments start getting a bit pricey as you keep going ahead with them, plus the extra health can prevent them from getting totalled in a battle.
What Isis has over Ra
Cheaper obelisks and faster building of them - really helps the early game scouting.
+3 population with TC's - when the game hits its peak with military units, this is VERY helpful
Prosperity - I believe prosperity is a more useful GP than rain
Better choice of minor gods - my favourite 3 minor gods acorrding to the ages they are in are anubis, Nephthys, and thoth, guess which minor gods ra lack ;/
Both have at least 1 major advantage over the other in my eyes (ra: empowering priests, isis: minor gods) and I'm having a hell of a time picking which one to use over the other (I do not like using both equally, I like to pick one and get as good as I can with it)
Help me with my indecision here with some of your opinions.