The beckon equivalent actually works fairly well if you're the first one in. I use it right away (after nebula) and then use the stomp equivalent about a second. The delay is because of the time it takes for the skills to hit, and I found that waiting instead of instantly casting had a better result. It's beneficial because the stomp generates aggression towards you, and also knocks down the mobs.

Commandos have a lot of skills that keep mobs knocked down but doesn't push too far. One thing I hate about the Operatives Lurch skill is that it often pushes the target out of range, even at lvl 1. I found that the commandos knock downs don't have that same large area push effect, however my "stomp" is only at 3 and I've never had it any higher on previous builds.

I actually really like the skill "Nebula" which is the 10 second AOE skill you said you saw no purpose in using. Yes, the mobs die fast, but again, if you're the first one in and use nebula first, the mobs will take continuous damage. After you knock them down, they're still taking damage. I have my nebula to 5, and have found it extremely useful and comparable to the Engineers "Transference" without the healing aspect. Hit's multiple targets pretty hard each hit and is good "background damage."

The one skill I don't like is the skill that shoots out directly in front of you in a cone. Yes, it's taunts, but it's really only good on bosses.

Don't bother with a high DPS weapon for the bosses. The operatives and even some engineers do enough damage per second to make up for yours. My commando is at 71 DPS or so, and I think it works out really well. Some of the harder bosses take very little damage per hit, and a weapon with more dps and lower base damage isn't gonna do much.