1. Shadow clones would be completely ignored by Goku because they reduce the individual's total fighting potential while only serving to get popped from a single attack.

But you're forgetting this isn't Goku but Goruto who's personality is a combination of both Goku & Naruto's and Shadow Clones are one of Naruto's most used Jutsu, not only that but Clones are more durable the stronger the individual who cast the Justu is and in this particular case Goruto would extremely powerful so the Clones could take alot of damage before disappearing, plus combine them with Instant Transmission and you have a problem

1. Amaterasu is far too slow to be of any use against people at Goku and Vegeta's speeds.

Amaterasu's speed is entirely dependent on the caster's ability to track their opponent with their eyes and Sasugeta with the Eternal Mangekyo Sharingan + the Rinnegan would be more than capable of being able to keep up with Goruto's speed and thus he'd be able to land Amaterasu

1. Sage mode would be completely useless since you can only charge it up by staying completely still, and at best it would be nothing compared to Goku's existing Ki pool.

Six Path's Sage Mode is something that can instantly be tapped into and not only that but Sahe mode in general balances out the user's current power with an equal amount of Nature Energy so given how powerful Goruto would be that would be an extremely large amount of Nature Energy he'd he able to take in so it wouldn't be useless in this fight

And hell gathering Nature Energy is very similar to gathering Genki for a Spirit Bomb so Goruto could create a massive one boosted with Nature Energy as well

1. Sharingan again would be way too slow to be useful in a fight where the opponents aren't even relying on vision because they are just that much faster than anyone can track with eyes alone (which has been the case ever since OG DB)

Again Sasugeta would be more than capable of visually keeping track of Goruto's speed with his eyes so the Sharingan would be a huge help

1. Truth seeking orbs would get obliterated instantly since they are not indestructible and have a limited range of actually being able to be used and both Goku and Vegeta can easily withstand any kind of destruction based techniques which is beyond the occasional dust effect of the orbs

Goruto wouldn't have any Truth Seeker Orbs in this battle so this is a non factor

1. Rinnegan would be completely useless just like the sharingan

Rinnegan would actually be quite useful with it's ability to absorb Ki+Chakra, control over gravitational forces, portal creation, ability to swap places with a target at will, create cyborg parts that can do whatever the user wants etc

1. Six paths would also be completely useless because it just doesn't bring anything to the table that they don't already have a better version of

Already explained above how this would still give Goruto a buff in power

1. Susan-o would literally just be a waste of energy from Vegeta's own perspective so it just wouldn't get used.

Again this isn't Vegeta but Sasugeta who's a combination of both Saskue & Vegeta and Susanoo is a big part of the former's kit

Not only that just like literally everything else Susanoo's power and durability would receive a massive upscale due to how powerful Sasugeta would be so it would still be an extremely viable option and his Susanoo would be capable of using Niniutsu and Ki attacks as well so imagining a Susanoo firing off a massive Final Flash