You can easily run U-turn on an Expert Belt/Z-move set to bluff a choice item, or you can just go for the raw power of a Choice Band or even run a bluff U-turn for purely momentum on a surprise Choice Specs set. You've pointed out yourself- the base 100s are quite mediocre currently, and most Garchomps I've seen refuse to run max speed in favor of bulk to abuse the fact that Rough Skin + Rocky Helmet makes for a hilariously painful anti-Metagross combo. The thing about Mega Scizor is that you KNOW what Mega Scizor does- it either takes a defensive defogger role, or it starts dancing and punching the fuck out of kids. (Kids not named Tapu Lele, that is...) You have zero reasonable expectation to what Genesect you're dealing with and the coverage it possesses in comparison. (Okay, maybe not zero- most are scarfed. But when they aren't, well, god help you.)
You're naming checks with some massive baggage of their own. (Notice the fire-typing? Notice how fire is weak to rock?) Congratulations. You managed to undermine your own point.
Alright, you're completely correct- if there are Pokemon you MUST keep in mind during the process of teambuilding, that's a symptom of centralization.
However, both Greninja and Pheromosa might as well quit when confronted with certain counters- there is absolutely no way for a Pheromosa, besides a previous Beast Boost to Attack somehow (This is the only halfway common scenario besides a Baton Pass), to bypass Toxapex and just about any bulky Ghost (Dusknoir hidden OP- hell, Gengar could probably come in on a HJK, live the Ice Beam or whatever, and Shadow Ball her into the grave). Likewise, Greninja is similarly walled by Toxapex and Blissey or Ferrothorn or- okay, you get the point. The Tapus all have their own baggage as well, in addition to all of them being vulnerable to Toxic Spikes: Tapu Koko is fast and gets free double STAB on Electric moves, but a Ground-type not named Landorus or Garchomp giggles at it, as does Alolawak. Tapu Lele can't be countered by Scizor, but its rather predictable movepool means that decent play (And Toxic Spikes) will bypass her easily. Tapu Bulu sometimes ends up helping the other team with Grassy Terrain and a quad weakness to poison is pretty fucking annoying when someone actually does take advantage of it. And Tapu Fini, despite being bulky as hell and a great defogger, can be hit by Toxic Spikes on the way in and really doesn't serve a purpose besides a decently fast Taunter and Defogger.
Can you say anything even close to the same about Genesect? Download means that it's always dangerous, its movepool is too wide to be codified into a standard set of expectations, its statistical spread means that it has good bulk and is on the high side in terms of speed, and one counter to Genesect with a scarf (Toxapex) is not a counter to a Genesect with an Expert Belt or Life Orb. I don't know of any other OU resident who can do an about face like that.
And yes, Toxapex is a bit of a problem currently (Regenerator + Recovery and absurd typing in a single Pokemon is pretty busted) but you KNOW what Toxapex does, you KNOW it has zero offensive presence, and it actually possesses very common weaknesses. Oh, and Tapu Lele.