I'm a lv. 35 BH Arsenal Merc (the mirror to Trooper Commando Gunnery) and I've been PvPing as one since Beta.
Here's a few tips to deal with a melee on you as a M-BH/C-Trooper:
1) Spec Tenacious Defense so your Concussive Charge has a 20 second CD and spec Concussive Force to make your Stormstrike a knockback and your Concussive Charge stronger.
Concussive Charge is your first line of defense. This knocks back all melee on you and slows them, and if you plan it correctly, you can knock back someone off the high ground and gain a huge advantage. Despite wearing heavy armor, don't be out there waiting to get snagged by an assassin/shadow. Gain the height advantage in almost every scenario that it is available.
2) Utilize your 4-second stun spell intelligently. Use it to set up a Grav-Round/Tracer Missile combo and deal a high health deficit. If a player is low on health and you aren't, they are going to retreat to start using non-offensive abilities to survive. This is your time to strike. You want to start the fight in your favor.
3) Use Concussive Round! It doesn't have to only be a CC for the healer. You can use it to open the door to getting some distance or setting a combo. In fact, you can juke someone into blowing their CC-breaker and then make them pay with a stun that really matters.
4) Use energy shield BEFORE you are below 20%. It's not going to do you much good to block 25% damage when you have 200 health left. If an assassin opens on you and your other escapes are on cooldown, use energy shield.
5) Lastly, but definitely not least, DON'T RAMBO. You aren't a lone killing machine capable of destroying entire armies of players. Help your team, assist in heals if you have to and focus on objectives. If you sit there spamming tracer/grav rounds and are totally unaware of your surroundings, you are a FAILTROOPER/BOUNTY HUNTARD. Don't be one.
Hope that helps.