Prime your very correct in the fact that most if not all decks do not need pachirisu. But think of the benefits of it. A very quick start for gardy gallade decks which rely heavily on claydol for draw power since they dont play many supporters of their own. They need claydol to rotate through their decks to bring other pokemon out. If they used Mentor they would have to rely on going second turn then using some supporter to probably celio's network to search through for claydol. It's a turn two at the soonest claydol. Obviously with pachirisu you still get the turn two claydol but you have the ability to play an alternate supporter besides Holon Mentor. We all know that the set-up stages of the match are critical and the faster a deck can get its main hitter into play more than often than they have a much better chance of claiming the victory.
Magmortar also doesnt NEED pachirisu but it's beneficial in this deck more than in any other I think. Using pachirisu to search out three basics usually magmar x 2 and a baltoy, or a cyndaquil instead of a magmar allows the set-up to start so much quicker. Then his purpose is still not served. He can attack dealing 10 damage(I know it's small but Dunsparce did the same amount with less HP, but still had the chance or paralysis)every turn just waiting to be KO'd. Your statement is that this just puts you behind. True it allows your opponent to claim one more prize than you but like most magmortar decks scramble energy is a behemoth of a card when your behind adding an automatic 60 extra damage. That's more than any energy has added to any pokemon in the game because of an attack based on amount of energy. Also letting that Pachirisu be KO'd allows you the benefit of controlling the field. Your opponent may be stuck basics and one solid evolution and when pachirisu goes you have the ability to send up whoever you want. I've also seen this really screw people over but IMO it's a benefit to send whichever pokemon you want up.
That's just considering the top two decks. You also mention the neither of the top two decks play any tools that stay on longer than a turn and No deck out there plays any. The reason they dont is because of pachirisu. Having the ability to deal an extra 40 and discard the tool? Lets face it most decks that play cess crystal use tank pokemon like empoleon, Lucario, and blissey who can take a hit and hit right back. It would hurt the deck tremendously to have a cess crystal taken off and then knock two more right off in your hand. Theres ways around keeping them in your hand for awhile and a good player would be able to rotate out his cessation crystals to keep them alittle more safe but they're sitting targets. Keeping them benched keeps them safe and if its benched then it doesnt work. Your opponent is free to use powers. Bringing them up all your opponent has to do is use pachirisu attack and can usually knock off two crystal this way.
You make good claims to support your argument, but the format is still in the T2- T3 stages. Were not out of it yet but when that changes alot of your points will be more valid, but not until the rotation. pachirisu is one of the best cards to allow an early set-up and I think will continue to be until we recieve a card that can do more than that.