Why don't we try to establish a baseline that we can all agree on? Rather then arguing about half a dozen separate things at once? No mechanics here, just things we all agree are important and necessary.
1) There needs to be some method of quickly taking down and capturing Standard Characters. It's just too prevalent in source inspiration.
2) This method need not be automatically available to all - it might require something like a "Police Training" feat (or chain).
3) To avoid anti-climatic scenes, Special Characters should be more difficult - requiring specific specialised training or abilities. Including PCs. New NPC qualities could also make them difficult / impractical to grapple - again, to avoid a totally anti-climatic finale to your mission. Please note that I'm not saying "Impossible" - just "more difficult"
For the above, compare various Melee Supremacy feats (and their auto save fail tricks), as well as the Misdirection chain (for comparison to abilities that can target special characters).
4) Certain grapple options can stand to be divorced from the subsystem - Screaming Club can easily be an "inflict and done" action. Personally, I'd feat-gate it as part of a "Monstrous Brawler" chain (but with a better name) - but it could very easily be a standard combat action (just like Trip or Bullrush). Same can be said for manipulating an opponent's gear - it can be a standard combat action (via Prestidigitation, perhaps).
5) Building on the above - Grapple, as a subsystem, should only have rules for grabbing hold of your enemy, and keeping them in your square. I'm specifically not saying it'll be a subsystem for just shutting down the enemy entirely - at this stage I am referring specifically (and only) to the ability to negate their movement by grabbing them.
We can put the Throw ability in with Screaming Club, or other "Inflict and done" abilities, and just keep the Grapple Subsystem as the practice of grappling - that way players can do things like manipulate their enemy's gear, or throw them, or other things without either mitigating the enemies actions, or it being impossible due to the enemy's size / strength / signature skill.
Thoughts? Are there some points that you find agreeable, but not others? I think if we can find some common ground that everyone can say "Yes, that is fair and does what I want it to" about then we can move forward more easily then if we try to put 12 ideas together at the same time. Foundation work, that's all.