Unfortunately, it's not just that it copies a permanent spell and not a permanent that's the problem. Myojin only gets the indestructible counter on it if you cast it from your
hand, and the command zone is not your hand. The only way I can think of in mono blue to get an indestructible counter on it without casting from hand would be either
Tyrite Sanctum or
Tekuthal, Inquiry Dominus (activated ability) +
Leech Bonder or
Nesting Grounds. Otherwise, you'd need either a
Campfire or
Command Beacon to put it from the Command Zone into your hand, or to spend the eight mana to cast it, more to bounce it back to your hand somehow, then pay eight again to recast it.
There are a few times where I've done something similar and realized that a card didn't do what I thought it did (because I didn't read it properly) or some interaction I thought was cool didn't actually work the way I thought it would. The only recent example I can really think of is
Liesa, Shroud of Dusk. She's the commander for my Orzhov Angel tribal deck. I thought the paying life instead of commander tax was a
may, but it isn't. You
have to pay the life each time. Turns out that you don't need a
Drannith Magistrate to prevent her from being cast from the command zone when you yourself played an
Angel of Jubilation. Needless to say, I took that card out of the deck in a hurry.
Has mtg ever made you want to beat your head against the wall and cry?
You mean that isn't the default response when playing Magic?