I read from this question that you don't have a counter for that?
Ranged characters. Someone with a big stick may fear someone with a bigger stick, if they're both well trained. Also, can't go wrong with some darkness and/or obscuring mist, or even put them into a forest. I disagree that the spiked chain is piercing, it seems more slashing to me, which if you house-ruled that then underwater combat would work well.
Pitting your players against anything in the available books is fair game, since they had the option to do that from the start. However, I've noticed when playtesting that any monster I hand-craft is notably more difficult than others of its kind, so I up the CR by one just for that reason. If I change its feats, this is especially noteworthy.
There's nothing wrong with feats being synergistic. It's called building a character.
One more question to factor into yours: Is this a finale, a major soldier, or just a grunt that they'll be fighting?
Usually in my game, I save the really sweet tactics for the big guns because they're so effective. A melee against goblins becomes much worse when each of them is disarming the characters, every time every combat. Gotta balance :) Remember as a DM you get to show off tons of creativity, not just the combat aspect. Gotta let the PCs shine too, they're helping make your world.