I am not exactly sure how or why Spartans are so effective.
Firepower - A Spartan has no more fire power than can be given to any UNSC Marine. They use exactly the same guns.
Protection - A Spartans energy shield offer a fraction of a second of protection from small arms fire in gameplay. In lore I think this is even less since an Elites shield only protect from 3 bullets. (Incidentally what exactly is the point of those shields if they only protect you from three bullets?)
Mobility - Spartans are extremely fast and don't tire. This also makes them extremely accurate.
So basically the Spartans only really exceed in the final category. Which is pretty much reflected in the books and in the games. If you just try to wade through enemies like a Space Marine from 40k even Grunts can and would kill you. The vast bulk of fighting relies on you quickly and efficiently taking down the enemy before they can respond with accurate fire and rapid movements. In the books, even the Spartan 2's get injured and killed by mundane weapons like Plasma Pistols and Plasma Rifles. This suggests that their armour and shields are mostly ineffective.
Incidentally, if you compare this to the advantages of a Space Marine:
Firepower - Armed with a boltgun that is vastly superior to a lasgun in every single way.
Protection - Power Armor that makes the wielder immune to most smallarms with solid protection even against heavy weapons.
Mobility - Marines are extremely fast and don't tire. This also makes them extremely accurate.
Basically Spartans are a problem because the Covenant and Prometheans aren't able to hit them. But they don't actually provide an increase in firepower or protection.
So why exactly does the UNSC invest huge amounts of money and material in this project if one Spartan is essentially just another Assault Rifle? You could probably train and equip a division of ODST's instead of one Spartan; they killed the same amount of Covenant in Halo: ODST as the Chief. So unless you argue the entire game wasn't canon, then Spartans are a bit of a waste of money.
I see where you are coming from, and to an extent I've also been thinking about this.
The thing with spartans isn't just how much damage they can put out, but what kind of operations can they pull of, how reliably and at what rate, both in success and frequency.
A highly classified operation, take First Strike or Red Flag, for example, has many requirements:
1. Minimum unprofessional motivations. Meaning no family etc which could compromise units efficiency... Spartans where kidnapped as children.
2. Has to know more about warfare than just how to point and shoot, extensive knowledge of tactics fighting on land, sea, air, space and in both non gravity and heavy gravity enviroments.
3. Spartans have to actually get to places which are restricted in ways no mere strenght can get through. This is where the AI step in.
4. The augmentations on top of extecive training since childhood... And a super armor on top of this... You can find every single detail about these with a bit of research in more detail than I'd ever be able to muster in 7500 words...
At the end of the day it does't just come down to how good one kills... it comes down to how much tactical value can be achieved with an asset. This manifests for example in high risk missions such as First Strike and in more indirect effects, such as in morale boost.
Hope this answers your questons.