"How can adding completely optional new content be the worst decision?"
It all depends on how it is implemented. If that new content creates rewards (as they say it does), then those rewards need to be carefully designed. The may implement it beautifully or terribly, and it is always easiest to implement something terribly.
Now back to your question, how could it be a bad thing? There are lots of ways. Even though they say it's fully optional, groups may find it essential to have specifically "skilled" members to create the best "skill modifiers" for that group. This would give the shaft to those who didn't opt to pursue this new optional content.
These new "skill enhancements" could be made sellable, creating a (previously absent) economy for CoH. This would make influence mean far more than it does today, greatly changing something we are all currently used to. Characters that solo and collect influence more effectively would rise yet another notch on the power pole.
I could site dozens of plausable examples.
Now, all this said, I have great faith in the developers, and I'm sure they will do their best to implement this system in such a way to avoid as many foreseeable pitfalls as possible.
As always, however, the proof will be the pudding.
