Agreed. He was more cut-out man than a long-term investment. That being said, if he /had/ managed to grow into bigger things (possibly after taking down a Council wizard or two) I've no doubt they'd have found larger uses for him.
I tend to think he was a Tool in a War of Prophesy, that the BC's main goal was to target Marcone and take him out before he could grow into whatever it is that Vadderung is grooming him to become (The Good King Johnny?). The whoel trust run of the Bloodline curse, and even the development of 3rdEye, were more side-benefits, but things that could have reasonably been accomplished anywhere (like a fully Ramp-dominated South America, perhaps).