The main issues with Machinists have little to nothing to do with the damage output of Machinists.The capability of constant ranged fire while on the move presents a huge advantage that most melee characters are not allowed to have. Parsing damage on targeting dummies only presents a stationary snapshot of the overall damage a target is capable of putting out. Boss sequences wherein melee fighters are unlikely to stay in range for several seconds at a time while ranged characters like the machinist can continue to fire at the boss is an advantage not afforded to melee. This is balanced by the lower damage output of ranged characters like the Machinist.
Instead, the issue lies in the frustrating mechanics and slap-a-dash skills that machinists have to work with. The machinist relies on a rigid set of skills and procs that lack the flexibility of the archer's supplemented with the bard's job abilities. Whereas the archer has a "circle-of-life" style of play with procs that work and build off each other (Heavy Shot criticals proc Straight Shot criticals, which in turn boosts critical damage which in turn boosts the critical chance of Venom and Wind bites which in turn refresh Bloodletters which is instant and can be used in conjunction with heavy shot and so and so forth), the machinist relies entirely upon a structured, chance-based skill chain doesn't build upon anything but damage. None of the weaponskills build upon each other in a unique or fun way. Instead, they rely upon a gimmicky and lengthy buff (one of several) to force a proc into the next successive attack. Worse still this buff plays into other attacks but does not do anything with them aside from boosting base damage by 20% (give or take a 10% or less increase in damage).
Coupled with the above, the machinist juggles far too many buffs. By itself, the machinist carries Assemble, Reload, Quick Reload, Rapid Fire, Gauss Barrel, and Hot Shot. Combined with cross class abilities such as Hawkeye, Raging Strikes, Blood For Blood and Quelling Strikes, the machinist is juggling ten abilities that are straight buffs. To say nothing of additional abilities used for the machinist's turrets, Rook's and Bishop's Promotion and Hypercharge. No class or job is juggling this many abilities at once. This is a fundamentally bad design.
Reload and Quick Reload are the core of the class design, but they are boring abilities identically similar to buffs like Blood for Blood or Raging Strikes. The main use of the reload buffs is to force a proc and increase the damage output of machinists. But abilities are boring and flawed in design. Unlike Dark Knights who can use Dark Arts and play with a number of abilities that enhance its damage or grant additional effects, or Summoners who are granted access to new and unique abilities, Ammo simply grants extra damage in the most boring possible - like Hawkeye or Raging Strikes. There's no "fun" to be had with Ammo, no unique abilities granted with ammo, no special damage over times, or debuffs. Even rogue's passive poisons buffs change up mechanics for Mug and Jug. Worse, ammo is consumed by every weaponskill and doesn't grant additional bonuses for being used outside of Split, Slug or Clean shot. Machinists don't recieve a better damage buff with an ammo used Hotshot, or a strong damage over time (DOT) with an ammo used Lead Shot. Ammo isn't used and doesn't affect abilities like Gauss Round, or Ricochet. In fact, it can be penalizing to use ammo on abilities like Hot Shot and Lead Shot as two additional rounds of ammo can be used to complete another Split, Slug and Clean shot chain.
There are, of course, additional issues. The debuffs the Machinist utilizes are many, and many share a cooldown. This would be fine as it presents a choice between which to use depending on the situation, but in reality, there's no real choice between using debuffs. Heavy and Bind are rarely going to be used as so many classes already have these abilities. Head Graze and Suppressive Fire have completely different debuffs, but Suppressive Fire suffers from a lack of range and in most cases Head Graze will be used instead. Only Rend Mind and Dismantle present a real choice, unfortunately, their lengthy cooldown prevents them from being more aggressively used like Virus, Reprisal, Rage of Halone, Dragon Kick, or Delirium. At least it stacks.
Other miscellaneous issues include the fact that many of the cooldowns that Machinists utilize are disjointed that its difficult to line them up properly for burst periods without sitting on them for a lengthy time. Opening burst rotations are obviously where most players focus on, but they aren't realistic in most encounters and instead of useful sustain is recommended. Unfortunately, the Machinist is lacking that as well and this is where the perception of low damage output comes in. Because of too many buffs and too many disjointed cooldowns and strong opening bursts Machinists are suffering droughts where they're literally twiddling their thumbs until an ability is and ready to be used to enhance the output of the machinist. These dry periods existed on other classes like the summoner and were finally addressed with the expansion, But it is apparent that the effort to fix summoner's down period did reflect or see equal attention to the machinist's downtime.
There are additional issues with turrets too. They're treated like pets in that they can take damage, but are stationary and must constantly be moved. There's not much indication how much range the Rook and Bishop turrets can cover. There's no real way to heal a damaged turret and they're vital to the overall damage output of machinist. They may have only one ability (or two if you count promotions), but it would be nice if they could follow the machinist around. Certain stats don't seem to affect turrets in the same way that summoner's pets do, either. But it is hard to tell.
Overall, a change of fundamental mechanics, less reliance on buffs, stacking buffs and cooldowns and some quality improvements on the mechanics of turrets would go a long way to fixing the issues with the machinist. Damage isn't really a concern, but improving the play and "fun" of the class would improve the attitude of players and machinists and may change their view on their damage output. Mechanically, the class is a mess and many simple changes are wanted and needed in order for the class to perform its best and change perceptions. Until these things are done, many players are going to continue to look at the machinist as broken job, but with the right changes, the job would be seen in a better light.