On reconsidering the issue, I have to say, Larian really did open a can of worms with source skills. Any time you have a limited resource that is very powerful, then you either have to balance the game with their use assumed, or not. But since they can't assume you'll use source on any particular fight, then every fight will have to be beatable without source.

The power armor conundrum as Neonevik says.

At most, they can balance Tactician mode so that fights are extremely difficult without source, and still hard with source, so every fight makes you question whether you should use source. But if they're going to go for the route that in general collecting source is somewhat evil except a few situations, then being good will be hard. I kind of like how being good might be difficult and involve sacrifice, as opposed to the opposite in most games, where being evil is difficult, but don't know if it will be too much to limit source by good methods too much.