Yes, I'm talking about a combo opposed to a single pokemon. As Greninja is glue to fill the holes of teams, it's there, like many others, to disrupt the combos between enemy members. Just like Rotom-W stops a combo of Landorus/Keldeo, as it checks and shuts off both, Greninja was feared, so the combo Heatran/Metagross wasn't applied much. Metagame is all about combos. That's why you don't just take 6 individually strong pokemon and call it a team.
When speaking of suspect test, you should take all sides into consideration. Let's see what Greninja really does.
It can be three things offensively:
a) A full special sweeper, with or without u-turn, usually carrying a choice specs or scarf
A physical attacker
c) A mixed grill
Choices b and c are not quite frequent, as Greninja is outclassed by other physical attackers and may serve just for a suprise attack. This can work only if applied mid-game, which is nearly impossible, since he'll have to appear when things get tough. He's there to get you out of the tight place, remember? Mixed doesn't work EV-wise, because it limits Greninja's destructive power.
So let's go to the usual and most frightening set that causes this suspect test; the special
Common set: Hydro Pump/Scald, Ice beam, Dark Pulse, Extrasensory/Spikes/U-turn
What does it do: Mainly hit hard faster than the opponent. That means, it leaves no loose ends. If it can, it will kill you. If you change and your switch is not bulky enough to hit faster next turn, or take the hit, you'll have to end up dead and wait for your revenge killer. Awesome in the offensive.
But wait there's more! That kind of thoughtless play actually proves to hinder teams outside of the field. When creating them in competitive play, people think of possible threats first. Some like to build around a certain pokemon, so to cover those threats, they would stop for a second and decide not to include some mon, that otherwise would make the spot, or put others, specially as a counter (which is an argument for suspect). Some others like to play around the members they choose in order to find out what suits their playstyle and to bring balance.
That said, Greninja limits the HO style some might choose, because it can be brought out to dish damage to pokemon relying solely on their speed, or worse attack or special attack. Most evident: it limits HO synergies (eg Latios&Volcarona&Landorus&&&...)
How can I NOT speak of combos?
Take a look at what used to happen a lot in Gen5. Dragons. Teams with 3 or more dragons that dominated the game. Even so, both teams had to make combos. The opposing team knew that the (then) almighty Garchomp or Hydreigon could sweep and prepared accordingly. Bronzong and Heatrans with balloons were more common than a mega is now (just saying), not to mention the necessity of bringing a Mamoswine to stop with priority ice shard, sometimes also banded. Now we have the same situation, just more balanced.
In the suspect test, most teams either have something to substitute Greninja, like Latios, or even Tornadus-t, or turn in general towards offense, seldom bulky.
About CroBro, I do know it's a thing and I've faced it a couple of times. It still didn't pose much threat. Taunt it, trick it, stick a water resistant pokemon against it, like Rotom-W or M-Venusaur, I still think it's not that great. I prefer normal bro, which can regenerate. The way I see it, it is not the monster they present it to be. Sure, if you let it calm mind more than you'd like, you can't crit your way through. If you wear it down fast enough, it doesn't have the time to rest or keep the health it gets from it.
It would be also devastating if it had a set: Calm Mind, Scald, Slack off, Trick Room.
You can use it with a clerk who'd get rid of status ailments or pass a wish (or a healing wish) to make it ready to battle, after the status-inducer is out of game.
eg Latias or Togekiss