The issue here isn't so much that Mach Strike is too good, it's that nearly every other deck is arguably terrible. I've always seen the decks as marketed more toward children/beginners. With decks like Mach Strike, that changed. You could buy two and instantly have a low-tier competitive deck that could be built up even more by adding other singles into it. This isn't true of most of the theme decks, save for Greninja back in XY BreakPoint.
You can't ban one theme deck that people pay real money for in real life from a game just because it is better. It would be a poor business decision as it would alienate players who want to play with a deck that is both actually good and features very popular pokemon/characters from the games/anime.
The real solution is to make each new deck moving forward just as good as Mach Strike. Other TCGs like Yu-Gi-Oh feature structure decks that you can buy 2 or 3 of and you can instantly start competing in local/regional tournaments to some degree. This is nowhere near true for most pokemon theme decks, and it's a real shame. I thought Mach Strike was a new era for theme decks but the most recent ones are back to being kind of lame again. Come on, TPCi, let's usher in a new era of theme decks and foster more exciting competition!