I think this comes down to both programs being vastly different for a plethora of reasons. To be entirely clearly, I absolutely love Spartan IIIs and am currently imagining my Infinite character as if they started out as one.
Now, on to the simple baseline; Spartan IIs and Spartan IIIs are both methods of making Spartans, but by almost no means similar. An individual Spartan III, in their intended gear, has absolutely no chance against a Spartan II in their own loadout. And this is fine. IIIs were never meant to be on par with a II.
While technological advances made the augmentations more potent and safer, one of the massive differences between the Spartan IIIs and Spartan IIs is their genetic curation. IIs were filtered out for the program in a time of peace, with stable medical records, ample time to collect data, anticipate reactions and synergy, etc etc, all so they could stretch the end result of their augmentations to the absolute limit. They were taken at a younger age and trained from one of the earliest points possible to be at peak human condition prior to receiving their augmentations. Now, even with all this preparation the simple fact that when something could go right for them, it went amazing because they could use those augmentations to their fullest, also means that if something went wrong, it would be disastrous. Just look at the numbers for their initial run at the augmentations. Half the IIs came out of it deformed or deceased. The other is the pinnacle of humanity’s fighting force.
The Spartan IIIs were recruited at the same age that the IIs got their augmentations. The pool of applicants were volunteer orphans because the army needed to burn the paper trail. The parameters for acceptable subjects were eviscerated as the bar had to be that much lower to even the odds in a time of war. While the technological advancements with the augmentations certainly helped, if the individual is only able to gain half the muscle mass compared to a spartan II subject, they only have a fourth of the chance for those muscles to shred their skeletal structure. A spartan III, given the context of who made up their program’s recruits, would never have the chance to get near as much reward from the augmentations while receiving far less risk from that exchange as a benefit. They also lacked the physical training prior to their augmentations, likely coming out in a similar condition to what a spartan II was at going into that program’s augmentations.
Going back to their equipment, SPI is not inferior to Mjolnir. It is made for a vastly different purpose which actually provides one of the greatest advantages available to the Spartan IIIs while operating in the manner they were trained for; Wholesale onslaught. A Spartan II, while raised up in a team and instructed in squad tactics and unit cohesion, is built to be a one man army. A Spartan III, while some members were spirited away for the likes of the Headhunter program, was always meant to carry out their missions as a battalion of Sam Fisher’s. Spartan IIs are sent around the battlefront in their groups to sway the tide of battles. Spartan IIIs are deployed as entire companies to raze Covenant strongholds deep behind enemy lines to the ground. Spartan IIs take the shock of attacks with their shielding to protect their marine allies. Spartan IIIs, with their invisibile armor en masse, are never being attacked until the fight is primed to be won whether they survive or not.
Alpha and Beta companies were wiped out because that is what their missions called for, removing an unmovable object by engaging it with an unstoppable force, in order to delete both factors from the equation. Be it an entire fleet of marines, several teams of Spartan IIs, or either of the Spartan III companies, no one was coming out of that situation alive. Yet, because of their purpose as a spartan program and the equipment they wielded, both Alpha and Beta accomplished their objectives while victory would have been questionable if the operation were attempted by any other force.
This brings us back to the scenario of a spartan II vs a spartan III. This is not a fair fight, because they are not equal fighters and were never meant to be. A spartan III will never be as strong, as big, or as fast as members of the spartan IIs were. That wasn’t the point. A spartan III’s augmentations weren’t as effective as a spartan II’s. That wasn’t the point. Their gear will never be able to take as devastating or as many blows as the Mjolnir system can. That wasn’t the point. They are not better than the spartan II program, because the two are playing different sports.
A special note on Gamma company. While they can likely put up the longest fight of any spartan especially now that many of them have access to mjolnir armor, I don’t think their specific drawbacks of a rapidly degrading psychological condition and the requirement of daily mood stabilizers is necessarily worth it.
While I can’t say that Spartan IIIs are better, I believe that chief says it best in Halo 5 when answering Fred’s question on Fireteam Osiris. “They are spartans.”
Now, enough procrastination on my bedtime.