Capstones are big, impactful abilities that wouldn't make much sense if they were active for only a part of the battle or can't be cleanly divided into three distinct levels. Thus, they can't be Boss Upgrades. Most of them have effects that are too powerful to have around on a low PL Boss, making them usable only by high PL enemies as a balance mechanism.
Aura of Misfortune
What I really like about Aura of Misfortune is that, rather than coming up with a brand new way to debuff the PCs, it makes use of rules that most players should already know of. Overheating and Unreliable can be viewed as a -4 to all Might Tests, because PCs ought to roll two extra dice to compensate for the risks of using those Weapons. It works very well with defensive abilities like Afterimages and You Are Too Slow, as forcing rerolls with extra Disadvantages and Overheating/Unreliable is the kind of tyrannical mechanic that superbosses should do.
Probably the coolest of all the capstones, because holy moly the Boss is huge you guys. The rules for such a thing have proven difficult to wrangle, though, mostly because this is a game where multiple Units can share the same Zone. If not for that, larger size Units would be a more frequent thing in BCG. The first version of this had a size of 4 Zones instead of 9, but that didn't allow much variety in shapes, so 9 was chosen to make it possible to have a 3x3 block, a long but thin snake-dragon-thing, or something more exotic like an X-Shape enemy. Its body counts as Extreme Terrain to represent that huge monsters destroy everything in their path just by passing through.
Embodiment of Evil
This essentially halves the total number of Genre Points available to the PCs. It's really strong and basically forces everyone to lose a bunch of Threshold Levels in order to fuel their Powers. Mechanically speaking I think the effect is fine... But Genre Powers are one of the most fun things in the game and losing the ability to use them kind of sucks. While this is a very powerful ability fitting for scary and oppressive major antagonists... It may be too good at its job of to the point of not being fun. I'm not sure this was a good idea, in the end.
This is very strong with builds that can make use of the extra energy... Which isn't that many, actually. The debuff effect is solid but it only weakens one PC at a time, leaving the other to beat the crap out of the Boss. It's okay, it does a good job of weakening only one PC for the Boss to pose a challenge but not be overwhelming, but it's probably the weakest Capstone without some serious optimizing to abuse the extra Energy.
When NPCs have sufficiently long range weaponry and speed, giving them the ability to 'kite' or hit the PCs while running away, can make them effectively invincible. Given how many movement abilities and long range guns Bosses have, this ability just couldn't be anything but a Capstone. It also wouldn't work well as an Upgrade because the ability to run away from PC attacks doesn't mean much when they've already been pummeling your Boss for a while. With all that said, the ability to kite is a 10 MP upgrade, so this gives a very large bonus to all Weapon Ranges to make it feel more Capstone-like and let the Boss snipe with Telekinetic Strikes and Technoleeches if they are so inclined.
Against most Squads, this messes up their positioning and doing some Damage and/or inflicting the Suppression debuff, which is okay. It becomes borderline unfair when there's a The Beast user among the PCs. Everything I said about Embodiment of Evil about potentially being too unfun applies here. The Beast is one of the abilities that are most in need of a hard counter, though. I'm not sure I like this but at least it doesn't spend Weapons and cripple Technique users like it once did. Now that would have been terrible.
And that's all of them. There's only six Capstones in the core book, because I still believed that if I insisted enough times that Operations should feature Grunts, Rivals and Bosses all together then people wouldn't try so much on running 4v1 Bossrush games. Like I've said before, I probably would have written things differently had I known how popular that 'gamemode' turned out to be. Hindsight is always 20/20, like they say.
I think Capstones do a lot to make late game Bosses (or early/midgame Superbosses) feel different from most Enemies by having big effects that change the rules of the battle from the very beginning. A proper 'Superboss' tier of Enemies would most likely start with Capstones or Capstone-like abilities then go from there.
Next: Allied Reinforcements.