I'd imagine that when upgrades came out and poison cards became even more effective - that outwieghed the disadvantage of poison's one and only true counter card going colourless.
That's really not true. Before upgrades, Poison decks with water mark were quite good, although they were more of an attrition build than a speed build. With Bone Wall at 3 Death quanta, the poison deck could stuff the deck with six and call it a day. At the time, the best decks were Queen/Rustler with Owl Eye, Alaska rainbow (because of how ridiculous Nova was), Rev's Time/Earth, Death/Water Poison, and a few others. Poison could definitely hold its own with the best of them. Now, any deck can use upgraded Purify to counterbalance the increased speed and power of the Poison build. The problem that exists with Purify is that it is a killer card against a specific deck type, relegating it to a mere sideboard card in pvp. Because of this, I think the situation with Poison decks is quite balanced.
As for the poll question: I voted for... (in no particular order)
Pulverizer - Okay, so Trident decreases the cost of Tsunami from three Earth to two Earth when upgraded to Poseidon. Eternity only decreases the casting cost from five to four Time (I happen to be quite thankful that the RT ability didn't get reduced, but that's another topic altogether). Pulverizer's casting cost is increased from three to four Earth, but
its ability falls all the way to just one Gravity from three. This is by far the best upgrade on a permanent, and you don't even have to go far for Protect Artifact. I would totally be fine with it changing from one Gravity to two.
Congeal - I'm actually torn between this and Supernova, but I figured I would provide an argument against Congeal instead of the usual "anti-rainbow" arguments everybody throws out there. Freeze is powerful, disabling a creature for three turns for an inexpensive one Water quantum. Congeal makes it four turns with no extra cost. Because of how fast matches are, those four turns can be long enough to effectively disable a single creature for nearly the entire match, or until the game is nearly won. And that's just one copy of the card, let alone how great it is as an ability on Arctic Octopus. I understand that freezing your opponent's creatures doesn't mean that you will win, but slows things down considerably so you can win much easier. My suggested fix is to make Freeze last two turns and Congeal last three turns.
Sundial - I'm not going to explain this, as I and many others have offered many explanations for this in other threads. Possible fix would be to revert it back to the bugged version, or to make it last only one turn.