I breastfed both of my children, but my milk wasn't flowing as much as it should, and they were both so hungry that I supplemented them with formula. They is so much pressure from everywhere these days to breast feed that I felt so guilty. But my kids are happy and healthy, so I let that guilt go.
My daughter was ok with milk-based formula, but my son was just like yours: very fussy, crying constantly and seemed to be in pain after every bottle. My doctor gave me a sample for Similac soy-based, and my son seemed to be better after that, but like you, I questioned whether soy was better than milk-based.
I was at Target one day, looking at the various formulas, when I came across Enfimil Gentlease. It's milk-based, but the proteins are broken down more, so it's easier to digest that the regular formula. I tried it, and you would not believe the difference in my son! He turned from this colicky, very unhappy baby to a very happy, joy-to-be-around child.
If you buy Gentlease at Target, though, it's extremely expensive - $25.00 for 24 oz. We discovered that Sam's Club carries it in 48 oz. cans for the same price. I know they carry it in the Golden Ring and Laurel stores, but check to see if a Sam's near you has it. Believe me, it's well worth the membership fee.