Where to even start...

Command Seals aren't absolute. Specifically, Illya is the only person who can command Heracles--and her command seals are unique--which shows that they can be ignored even without special NPs. Magic Resistance operates against Command Seals as they're magecraft--Gil's MR rank is actually based on the Archer class and his Master; it doesn't count how many items there are. At which point it takes an instant for something from Gate of Babylon to remove your head, break the contract, and negate the command (of course assuming you even get the first command out without it being predicted in time).

Secondly, you fundamentally misunderstand what Mystery is. It's an innate quality of something; power granted by the Root--it's romanised as Mystic, as clunky as that sounds, for a [i]reason.[/i] Things that exist long enough innately attract more power and that only increases with time. Being common knowledge does not weaken it; the only time implications like that are ever suggested are because of the idea of too many demands on a finite amount of power. Obviously, Fusang is such an odd nexus that it can't tap itself dry so it's fine. And magecraft isn't really going anywhere because not everyone is a magus and the actual systems are less important than the rest of it.*

Older = Better is the supernatural law of the Nasuverse and that's how it works.

*Also, this perfectly explains how Extra became Extra: exactly how much power do you think it takes to try and resurrect the first Dead Apostle [i]early[/i]?