It's pretty late here, so that may have come off as more dismissive and argumentative than I meant it, but there's still some truth to it. The drawback is inherent in the difficulty level of actually achieving the perfect board state to perform the attack.
Let's break it down. As any Greninja player can attest to, simply managing to get 3 Frogs on the bench on T2 isn't exactly the easiest thing in the world. You can start the wrong Poke, you don't have a ball search card in hand or the energy card to perform the attack, or even worse you have multiple Frogs in your hand or multiple copies in your prizes. Luckily, you try to Bubble with Froakie to try and buy a turn or 2. I don't think there's a Weedle with that kind of stall potential, but, for arguments sake, let's just say there is, and let's imagine you hit the nuts and T2 you get Kakuna, energy, and flood your bench.
Next turn, assuming your active Kakuna didn't get knocked out of course, you then have to find 4 Beedrill. Again, as a Frogs players myself, I've gotten 4 ninjas out at once before, but it's rare, VERY rare, and if you do, unless you prize all your BREAKS, you're gonna win. Simple as that. Anyway tho, so let's say you are the luckiest person on the planet and get all your kakunas evolved into Beedrills, attach a 2nd energy to your active (Greninja only needs 1 energy to use 2 different attacks), then you can snipe for 160. What exactly are we hoping to hit with that? Not a Shaymin. Not a Lele. A Marshadow maybe? Then next turn, assuming your 120 HP stage 2 didn't get knocked out, you can do it again. So you're 2 shot-sniping.
Let's look at it another way. Greninja is tough to set-up, but once you do, as the game goes longer, your chances of winning grow exponentially. You can set up OHKOs with Shuriken, even take 4 prizes in a turn.
With Beedrill, you have the same laborious set up, but without the benefit of a hitting heads on a Bubble flip, without the benefit of 2 different 1 energy attacks, without the benefit of an insanely powerful BREAK with a broken ability, without even the benefit of Splash Energy, so that when you start losing Pokes (which you will, almost every turn), you get to keep rebuilding your army over and over.
It just isn't worth it, unless they print some busted new Beedrill. Just my opinion tho.