I'm not the anon who's been raging about it but I think you guys are downplaying how powerful villains really were early on. Villains were key to the Two towers deck that allowed you to constantly turn your villains face down and reflip them to keep your opponent out of play. It was also key to the orange Kill your own villains deck. Once again by set two only 3 villains existed, 2 of them were ultra rares and you needed 3 of each for the deck to work at all. Set 3 and 4 also only added one new villain each both also URs. As far as mind games while placing a trouble maker face down, they were once again very important. More telling is the fact that troublemakers were hardly used outside of villains, except for the also very toxic yellow parasprites, since they were also supposed to be a core mechanic.
Also, let's talk a moment about how bad the starter decks were. You only bought them to get the mane character cards and the Fixed cards that didn't come in packs, so you were playing $10 for about 14 cards. They weren't structured or themed so they were complete garbage if you played them against someone who had done any deckbuilding whatsoever. Compare this to Weiss Schwarz where most players have seen people win a local tournament with a starter deck. In Weiss Schwarz the starter decks don't contain cards that aren't in the regular set, but every card has alternate art so they're still worth picking up for collectors.
What it all really comes down to is card symmetry and how the mechanics interact that made it pay to win. Also ultra rare distribution was a mistake on set one, a mistake from which they never recovered the loss of faith from their customers. UR distribution nearly killed MtG. The people designing this game said they played MtG so they should have known how badly this would affect their game, but they were after those brony bucks rather than trying to make a decent game.