Why are the stages in this game so littered with Injured Reploids, when other games in the series have lacked such a mechanic? Because of Isoc's speech. Random volunteers and mercenaries have come from far and wide to assist in the Nightmare investigation, lured by the promise of High Max's protection, only to be abandoned to the Nightmare to be corrupted. When Gate said he wants a society of only high-grade Reploids, this is what he meant: enslaving the "weak" to let his own elite caste reign on top.
Metal Shark Player can reanimate dead Mavericks from as far back as the SNES games, even though the bosses from the previous two games should be more powerful.note And also they'd have existing sprites whereas the SNES bosses would need to be remade. But, then you remember that the X4 crew was obliterated in space with Final Weapon's destruction, and the X5 crew was probably too damaged from a combination of the Sigma Virus and the immense pollution of Eurasia's fall. Player can't revive anyone if there's no body to revive.
Crosses over into Fridge Horror if one considers how many more bosses could be salvaged, if Player or another DNA resurrectionist wanted to.
Metal Shark Player arguably takes after his master the most, being a skilled DNA manipulator and an unabashed mad scientist. It's possible that Gate even got his help with some work, such as on the Zero Nightmare, considering how Player tells Zero he no longer needs to examine his DNA.
The descriptions of Blaze Heatnix and Rainy Turtloid. The former is described as being far more powerful than his coworkers and would ignore them even when they were in danger, causing others to want him powered down so he'd learn to work with others and value their lives. Gate refused and Heatnix was killed. Then we have the latter who had ridiculous defensive abilities compared to others, but he didn't do anything to bother his coworkers, it was just his defensive capabilities. They wanted him downgraded to be just like them, and when refused, Turtloid killed himself. The brilliance? The ones who wanted them dead did so out of hatred and jealousy respectively. It makes you realize just how human Reploids really are when they suffer from such a petty emotion as jealousy.
Gate's strategy as being a Puzzle Boss / That One Boss makes sense given his specialty. He is an incredibly analytical engineering genius with a track record for optimizing Reploids to dangerously high levels. It makes sense that he would have such powerful armor and such a dangerous strategy, putting the Hunters into a pit-filled arena and making himself nearly invincible. His strategy is just that good. If his own attacks weren't so strong against himself too, Gate would likely have been able to overpower them with ease.
If Isoc is indeed another form of Dr. Wily, it's possible he teamed up with Gate because he was actually following up on his team-up with Sigma in Mega Man X5. Either Wily wanted to salvage his previous plan by fusing Sigma's remaining virus with Zero, or he was using Gate to find Zero. If it's the latter, then he released Sigma as a distraction to cover for his escape; when Wily abandoned the Isoc body the Hunters prioritized Sigma instead of tracking him down, with Wily encouraging Zero if the player used him to fight Gate.
There are a few reasons why the research team didn't kill Gate along with his creations. First is that with Dr. Doppler and Repliforce's R&D gone, the world needed as many experts as it could get, even if kept in reserve. Second, they had no way to do so without arousing suspicion, since the research team relied on "accidents" or got lucky in some cases. Third, it's a safe bet the research team was under increased scrutiny after Mega Man X4. Fourth, they either just assumed Gate dead or lost track of him after Mega Man X5. That or someone was covering for him the whole time...
It's quite disturbing how the conclusion for dealing with Gate's overpowered Reploids was to conspire to euthanize them, rather than simply trying to get them fired or repurposed. Gate abandoning the team to live in isolation makes some sense when you consider this barbaric turn of events.
Another interpretation is that killing Gate's Reploids was deemed necessary. Since Gate was trying to make Reploids on X and Zero's level, the earliest they'd have been made would be right before Mega Man X3. At that point, X and Zero would both be proven warriors, and it explains why Dr. Doppler didn't target Gate or his creations. That puts the slaughter sometime between Mega Man X3 and Mega Man X5, during which Mega Man X Treme 2 and Mega Man X4 happened. Hard to blame the research team after all of that happened. Repliforce's actions alone probably exacerbated the decision to kill them. It also makes Gate considerably less sympathetic: if he refused orders in the face of all that, what choice did his superiors have?
In the end, Alia is left with the choice to resuscitate Gate or not after Sigma mortally damaged him. Seeing how he's never mentioned again, so much for that!
To be fair, until the Mother Elf from the Zero series, there had never been a case of somebody being completely cured of the Maverick Virus. That and the fact that even before he went nuts, he wasn't the friendliest of Reploids, as detailed above. It may simply have been kinder- for him and the world at large- to let him stay dead.
The reason Sigma is such a wreck in this game is because he expended himself spreading the Sigma Virus so far in Mega Man X5. Alia mentioned back then that the stress would have killed Sigma for good. This means that had Gate not purposefully put him back together for his little backup plan, Sigma would have ceased to be a sapient threat, and X7/X8 (or at least X7) would never have happened. Damn it, Gate, we were this close!
Commander Yammark died because he crashed after his flight system was sabotaged. This conflicts with the plot point of Gate's creations being too difficult for anyone except Gate to analyze. Or rather, anyone except those on Gate's level, such as Isoc/Dr. Wily. Wily took advantage of Gate's stubbornness and caused Yammark's death, which gave the research team the push they needed to go on their murder spree. Gate, his creations, Alia, and the entire research team were manipulated from the very start by a monstrous old man just so he can settle a college grudge without worrying about some young upstart who could discover Zero's secrets and sound the alarm.
