After taking a look through pkmncards.com, I think the clear winners for grass stage ones are Yanmega and Ninjask/Shedinja:
Yanmega Prime: https://pkmncards.com/name/yanmega/#images-9
was quite good in competitive play in its time, and I'd be more worried about it being overpowered than weak, but none of its attacks are particularly threatening. Zero-energy attackers are just always pretty strong, and "unlocking" it on this card takes some skill, as well as offering interesting opportunities for counter-play for the opponent.
For the second Yanmega, I would go with https://pkmncards.com/name/yanmega/#images-11
, which seems fairly solid, since you can power it up in one turn with a grass from your hand and grass from your discard, and immediately do sixty damage. Then after it gets hit by the opponent's dude, you just retreat for free and save him for later, when he can again power up in one turn to finish off one of your opponent's attackers. Or you can store up energy longer and end up doing 80 or 100 at once, if necessary.
This one is probably too strong: https://pkmncards.com/name/yanmega/#images-7
. It takes a pretty long time to power up, but the second one of your attackers dies, you can avenge them with an 100 damage attack, and again, once your opponent hits it, you just retreat for free and save it for later. In the end you'd probably get two 100-damage attacks from a single stage one, all at the price of just three colorless energy, so I think it would be pushing it a bit with the power level. Also, it would make the Yanmega line effectively colorless, because Yanmega Prime attacks for free in the right conditions, AND it combos very well with the Yanmega Prime, which retreats for free too, since you can repeatedly swap between attacking with each. The other Yanmega with Yanmega Prime is still a potent combo, but much more fair.
If you want to try something more wacky you could do this Ninjask https://pkmncards.com/name/ninjask/#images-4
with this Shedinja https://pkmncards.com/name/shedinja/#images-5
. Ninjask is a strong attacker if you can switch into something like Spiritomb, Jirachi, or most likely, the Shedinja that you just found with its ability. The Shedinja has a really funny ability in this cube, because (I'm assuming you're just treating everything that talks about abilities as referring to poke-bodies and poke-powers as well and vice versa?) pretty much every strong attacker has an ability/poke-power/poke-body of some sort. This would force the opponent to use some random prior evolution of one of their Pokemon to kill it (which isn't too difficult at 60HP, so it stays fair). Not sure if you're interested in play patterns of this sort, but definitely an interesting space to explore.
Yeah, that is the Mew I was talking about, although if you ended up putting in the Alolan Vulpixes, it might be too weak by comparison. I was envisioning it as a starter when something like Cleffa isn't present in your opening hand, that serves as a nice little free-retreater later in the game, and every once in a while slays some Psychic-type that's weak to other Psychic types. However, most of the strong Psychic attackers are weak to Psychic, because the Dusknoir and Gengar lines are weak to Darkness instead, and it really doesn't stack up to Alolan Vulpix. That said, Alolan Vulpix is really, really good in this cube (also might cause confusion with the Ninetales), so it might be better to keep the Manaphy in instead. In this case the Mew would look a lot more reasonable, but could still end up being too weak and not worthy of being played.
I agree that SPs and LV.X's are probably more trouble than they're worth. I really like the elegance that the cube has right now, in both design and with the drafting rules you've selected.
One last note; you should probably give your Gyarados drafters two Magikarp for each Gyarados drafted, or even as many Magikarp as they want, so they can play extras and try to get them in the discard for Tail Revenge. Gyarados's other attacks aren't great, so they probably need to be able to get two Magikarp in the discard pile for it to be a really solid attacker. Also, this Magikarp: https://pkmncards.com/page/2/?s=name:magikarp&display=full&sort=date&order#images-2
might be a better one to have in your opening hand and actually start with, since it helps you set up a bit faster than the current one, and when it dies, it will be fuel for Tail Revenge.