Gunnery versus Marksman

Well, its the same reason why Marauders do more damage than Assassins.

One is a pure dps class.

Quick notes of mine. Reestablish range is primarily used because it also contains the knockback on SoS/Pen. Granted for team ranked this talent's value would be depreciated. If you don't take that the remaining options would be the instant snipe or Flash powder, and assuming they haven't changed Flash Powder since 2.x that accuracy debuff works on Force/tech.
It's only bugged for snipers, it works fine for slingers. Although sniper's does have some effect. One person I know told me it only applies the DR to the base damage, not sure if that it valid or not. Either way for a balance discussion its probably better to assume the ability is working properly since bioware will eventually get around to fixing it.

The cover preq on the sniper's knockback is not significant. Crouch is off-GCD so you can easily rap it and hit Cover Pulse at the same and in the same moment break cover and keep running. Disadvantage being you risk putting Ballistic Dampers on ICD.
Also it's worth noting that mercenary's (not commando's) knockback has a definitive ~3/4 second animation delay.
Last time I checked Scrambling field stays in the position it was dropped.

I've said this before and I will say it again. Enet is hugely over valued. The only class it has major value against is sorcs. For everyone else it's typically better to just hardstun them.

I will give you cleanse.

Off-healing, ehhhh yeah the burst healing is nice when it works, but it's also fairly easy to shutdown. Besides have you seen the PTS? They are removing DPS mercs ability to burst heal in 3.3.

The Herioc teir utilities are especially bad since you can't take stabilized armor and reflexive at the same time unless you want to drop Forced March which would kill your mobility. Losing Reflexive leaves the commando that much more vulnerable to pressure comps and reduces the availability of the go-to mitigation DcD. Losing Stabilized Armor leaves the merc extremely vulnerable to hardswitch comps. Doubly so against MM burst comps since decoy doesn't do jack against Ranged attacks.

Another thing that wasn't touched on previously is that Sniper's Flashbang is instant with 35m range while mercenary's is casted with 30m range.

Snipers are not weak lmao... They are by far the best DPS class in the game.

Have you tried them in yolo ranked? Or without team support? The best dps class in the game... This is must be a top secret class (2 snipers on first 3 pages)!

This really makes a lot of sense now that I think about it specifically for these 2 specs. My question is what exactly would be done to make gunnery different in a significant way?

htl and enet are pretty fundamental differences. a mando should be harder to los than a MM sniper, but in the real world, I guess not.

make htl last longer. make self healing more relevant. I wouldn't touch enet as that can really wreck other formats. also maybe make armor rating relevant?

Let me highlight something for you.

That pretty much speaks for itself.

Armor rating and damage taken while stunned are very relevant. That's why an operative and/or assassin shred through a sniper whose entrench are on CD.

For example: look at assassinate from a hatred assassin. Assassinate against a sniper who is stunned will do around 10-12k damage. Assassinate on a merc who is stunned will do around 4-5k damage, because of damage taken reduction while stunned, and heavy armor.

The main thing that sniper is much better at than commando is anti-warrior melee. However, warriors are rarely used in team ranked, other than an occasional carnage mara, which a tank can easily keep taunted.

Also worth noting: commando is much more effective against sage than sniper. A sniper can't do much of anything against a sage that knows how to kite, because anytime the sniper hits the sage for that "epic 20k burst", the sage is going to LOS behind a pillar, use benevolence twice, then rejuvenate, while dots are still ticking on the sniper. If the sniper leaves cover, he is now vulnerable to stuns.

This is a perception issue, not a reality issue.
People THINK sniper/slingers are weak because there arent more on the leaderboards, but they are not. The reason we dont see more of them is not weakness, but the fact that people can do more with other classes in terms of overall utility, specifically, Sorcs.
Sometimes people take too much at face value and forget to think.

Fundamental difference is that the 2 second cast of Ambush allows an opposing player to prepare for Ambush damage. For example, if I'm attacking an operative, I have to "bait" their roll so they waste it before I fire my actual Ambush. You don't have to worry about that, because an operative isn't going to roll a grav round with no cooldown.

It's always a "perception" issue when it's not your class and an underpowered issue when it is.

EDIT: I want to make it clear that I'm not suggesting Commandos/Mercenaries are fine, but I do find it odd that you guys are targeting a class that is doing abysmal in solo and mediocre in group (despite our reputation in ranked, our top sniper sits at 1738, underneath every class but you guys and marauders). Playing a gunslinger/sniper in ranked right now is not an enjoyable experience by any means, and not something you really want to put as your goal post.