As for magic scales, I know rather little amount of situations when neutral or drain scales should be taken. I think that it is almost always better to sacrifice something else and take at least magic 1. Pythium has not bad research overall..
As for the questions.
1. I can't tell you what the exact steps in the early game you should follow, because I didn't experiment with Pythium much, but your troops are very good against indies. Recruit alae legionnaires, put them to the bottom on "fire closest" and add two or three replaceable arrow catcher units for each fight. This is a very good army for early expansion, especially with prophet, certainly.
2. Well, the answer depends on what you're trying to reach. Early research is important if you are aiming for something early. For example this may be Const for items or Alt for boosters on SC. It is true for any race and any game. So if you don't need early rapid research, then you don't need ArchTheurgs in early turns. And (it may sound blasphemous) may be you don't need mages at early turns at all, depending on situation. Having no mages at 2-3 turns and a fast expansion with second castle may appear a better benefit then early research. I suggest you to try a build I've proposed for Man here
http://www.shrapnelcommunity.com/thr...&sb=5&o=&vc=1. However, this build definitely needs research as you need reinvigoration on your Earth mother if you want to use her as a good fighter. If you don't rely on her as soon as she awakes, you may search sites for some turns. Everything depends on situation, as I already mentioned.