Excellent pointers. Thanks, guys.
You're most welcome. I hope the following is also useful.
As for the PL, I'm remembering my days of playing Champions, where agents could be dangerous to a PC. As far as I can tell, the lowest PL at which someone can be dangerous to a PC in M&M (in combat) is PL 6.
Oh, agents can be dangerous. It's all about how they attack and how they fight.
Example: PL 4 terrorists lay in ambush for the hero(es). They see the hero(es) and take time to Improved Aim, then strike from surprise. So, the hero(es) are on a flat-footed defense (typically ~15) and the terrorists are on a +8 to hit for +4 to +6 damage (70% chance to hit, 60% chance of +5 damage, 50% chance of +6 damage).
If those same terrorists Combine fire, that's another +2 damage per combining terrorist, quickly reaching +10 to +16 damage. Even a Powerhouse hero is going to be in trouble from that kind of opening attack.
HYDRA utterly relies upon Combine Attack to have a chance at actually dropping heroes. When twenty guys are hitting you at about the same time, it is danged likely to hurt even if they are only hitting with college-athlete strength.
Or you can cheese it up by giving them low-rank super powers, net guns (Snare gets mean quickly), and other unusual effects. Mental Blast (and the other mind ravaging powers) are extremely powerful against most heroes.
FWIW, Brubaker's Captain America (Bucky) seems to take quite a while to go through a knot of four agents, so they're not that "minionesque."
Well, Bucky is "only" doing +4 to +8 damage, which is a DC 19 to 23 toughness save. That's nasty, but a PL 3 can make those if he's lucky. On the flip side, a PL 15 can get messed up by those same damages if he's unlucky (assuming he's not very Impervious, which is uncommon in Marvel).
Regardless, good luck.