Uh...the Factory Head in Emerald was Noland, not Thornton. Thornton's in Platinum. At any rate...the Battle Factory is all about knowing your weaknesses and covering for them. If you had a bunch of Grass-types, I can see how a Pidgeot and Arbok could give you trouble. And that's why you keep a Steel or Rock/Ground type on your team to counter Flying and Poison types.