As I said, bullet/Shooter spell that has only been a demonstration and barrier jacket/Knight Armor that I can barely remember being used except during the demo with the ANBU and against Orochimaru. From a cinematic perspective, the least impressive spell he has. Flight that has been referred to but rarely seen, I think the only time was during the ANBU testing.
I get that Team Yurei is an infiltration team, I do. But there is no reason we couldn't see spells used during their infiltration missions alongside jutsu. So far we haven't and so the story just doesn't FEEL like a crossover to me. Replace the magic tome with a masterwork of Uzumaki sealing, just like Sarutobi believes, and the story would be almost entirely unchanged. That's why I said the Tome felt like it was little more than a deus ex machina to push the story in a different direction.
The fact that they are an infiltration team is
exactly why throwing around big, flashy, and highly distinctive abilities while on a mission is a
bad idea. If it's a covert information gathering mission the goal is for the enemy to
never know you were there. If you're throwing around battle magic will nilly, then you probably already failed your mission. Any intel you did get is now suspect. And if you're on a False Flag mission then the goal is to accomplish your goal and
blame someone else for it. Using flashy and distinctive abilities means that your enemy knows exactly who to blame, thus negating any chance of your secondary goal of placing the blame on someone else. Thus you want to use abilities which can reasonably be credited to the person or group you're framing.
And remember, Naruto is
not a mathmatical genius capable of creating an entire magic system from first principles and "there's evidence suggesting this might be possible using multi-dimensional math" like what's happening in Hybrid Hive. Nor is he good enough at math to modify a spell on the fly to create something entirely new. He struggled to learn each spell the Tome had in it's data base. Those spells are a basic Bullet spell (customized as exploding kunai), flight, barrier jacket, and a set of Search spells. As Minato put it, the basic beginner package was all that was left in the database due to damage. Even the personality imprints turned AI assistants can't modify a spell on the fly. Not only that, but they are limited by their own knowledge and what the Tome possesses. Thus the majority of Naruto's capabilities are sealing and jutsu because
that's what his parents and the Nine Tails know. And that's what he has around him he can learn.
If the Tome had landed in the Slayers world setting, it'd have access to the magic of that setting. If it'd landed in the Ranma 1/2 setting, it'd have access to the magic of that setting instead. But no, it landed on Naruto's world, so it's got access to the magic of "ninja arts" of the setting rather then anything else.
In regards to the clone bodies... As I understand it, the difference is as followed:
The tome of Night Sky had living physical people placed in it to form the Tome's guardians. If Nanoha hadn't resisted and pulled her Deus Ex Machina to escape along side the Tome's current owner, Nanoha may have eventually ended up as yet another of the Book of Darkness's bound guardians regardless of if she wanted to or not. The self defense program as I understand it had decided Nanoha was too dangerous to fight, but would make a good guardian.
Minato and company on the other hand are just personality imprints turned into AI assistants. They were chakra/mana constructs to begin with, and when the Tome of Orange Sky absorbed all that chakra/mana, the personalities no longer had a body to call their own. Thus there was no template for the Tome of Orange Sky to use for creating guardians. Now it has a template, but said template is based on shadow clones which are fragile as hell rather then a living body.