Interesting post.
1. I'm running two sets of characters, so I'm not yet far enough to be overleveled. I agree that it's not likely level changes will make it into the EE as it's a big balance change. One simple way to avoid overlevelling in Tactical in D:OS 2 might be that extra enemies simply do not give XP. That does have the drawback of being unsatisfying.
A better way would be to adjust the XP of each encounter in Tactical to give the same amount as normal. Basically, take a bit of the XP from all of the regular monsters and make that what the new enemies provide.
2. Do enemies farther along gain higher resistances to status effects? That was the case in vanilla D:OS, so I would assume that would also be the case in the EE.
3. I think another difference maker in boss encounters often comes down to having several party members and only one boss. You can get to take 4 actions for each one the boss takes.
4. Interesting idea for adjusting the AP costs of grenades. That's something that deserves more looking into. Right now I'm making a Grenadier character who will try and attack with mostly grenades.
5. Yeah, I'm not sure why Bitter Cold needed to be buffed, and it is silly that there are 5 Novice water skills when you can learn a maximum of 6 and 7 Adept water skills when you can learn a maximum of 4.
I'm not sure I agree with your suggestion to make Pinpoint a Scoundrel 2 Talent, never mind Scoundrel 3, since it's basically mandatory if you plan to use Grenades.
I don't see how boosting the Scoundrel level would promote the use of Rogues. If a player wants to use a Rogue, they will, all increasing the requirement of Pinpoint will do is reduce the options available for other characters. I don't think Rogues need special promotion.