This is an "All Classes" problem: cooldowns could use some tuning. Some abilities are blatantly more powerful than others. Pulse Grenade runs away with the prize of "Only Grenade That Feels Deadly". Yes, the other grenades have their uses, but EVERYTHING from that one grenade -- from the damage to the duration to the screen distortion -- is top-notch. Don't even get me started on immortal Devour Warlocks (which I play). I don't think any other subclass in the game has such an amazingly powerful mechanic available to them. Here's the thing: these aren't gameplay issues that need nerfs -- the are actually good examples of a baseline that ALL abilities should be at. ALL Grenades should be deadly. ALL subclass perks should define how that class plays. Guardians should be able to dive straight into the middle of a pack of angry enemies and go nuts. As an example, here's how I would add to Nightstalker [Way of the Trapper] Hunters: Dodge recharges on precision kills (including melee precision kills). Melee attacks from invisibility lunge farther and deal extra damage. Precision shots from invisibility deal bonus damage. Directly sticking a Smoke Bomb to an enemy disables their shields. Here now is a Hunter that is a terror on the battlefield, running around like a Predator and attacking in a flurry of Smoke Bombs and Grenades. The subclass would be a competent flanker in PvP, moving in to clean up kills and disrupt enemy lines once the battle was joined by their allies. Alternately, they could act as a long-range scout, picking off targets with precision shots and using their dodge and the invisibility it provides to relocate. Beyond these ability changes, all subclasses need shorter cooldowns. There is no reason for grenades and melee abilities to be available on timers that are a minute or longer. Class ability cooldowns should be "shortened" by giving each subclass a unique way to "cheat the system" and lower their cooldown or directly refresh them through a gameplay mechanic (similar to the Nightstalker suggestion above of Dodge recharging on melee or precision kills). The shooting aspect of Destiny 2 is great, but the things that differentiate Destiny 2 from other shooters -- the class abilities -- are lackluster in terms of impact and availability.
I like where your head's at, but the fact that you chose Nightstalker for your example is a little bit tragic. It currently has some very high PvP performance statistics, and Jon Weisnewski doesn't share your enthusiasm for fun.