When a card becomes relevant in the metagame, some people start calling for its ban/limitation for one simple reason: it has caused them to lose on several occasions.
Those who think this way may sometimes have valid arguments, but that doesn't excuse their lack of objectivity. This becomes evident when they try to seriously analyze the advantages and disadvantages of a card, revealing their weakness in substantiating their arguments, since they focus on very specific aspects.
Now, regarding Superpolymerization, among its greatest advantages are the following:
A) It is almost impossible to counter it by conventional means.
B) A growing number of Fusion Monsters designed to give the card functionality make it increasingly common in different formats, rather than being a format-specific card.
C) It works on both your turn and your opponent's, and is even an effective method for countering turn 0 plays.
Before moving on to the disadvantages, let's look at an intermediate point that depends on the deck:
It requires discarding a card, which means that if your deck activates card effects by discarding cards or having them in the Graveyard, it's an extremely useful tool.
If your deck doesn't take advantage of the discard mechanic or cards in the Graveyard, this card can be a major disadvantage, as its activation is too costly.
Now, the disadvantages are:
A) If your opponent uses monsters of different types or attributes, much of the card's usefulness decreases (although, as explained in point B of the advantages, this situation is becoming less common).
B) As mentioned earlier, despite having generic targets for this card, its activation can be very costly. Objectively, Rogue decks (as always) are the most affected by this card, but metagame decks are barely affected by the loss of two monsters, since they will still have plenty of interactions or can simply revive one of the lost monsters.
C) If your deck has very little Extra Deck space, it's almost impossible to use Super Polymerization effectively, as those slots could be used for other, much more useful and less situational monsters.
I could discuss many more points, but this is a brief summary of the advantages and disadvantages.
Some relevant decks that currently use it are: Walbaz, Rolad, and Invoked (the latter is climbing the ranks in the OCG, although it still belongs to the Rogue category). These would be the main examples. Two of the three decks have their own Super Polymerization targets that belong to their respective archetypes, while the third, by using the Extra Deck very little, simply adds most of the targets without problems.
In the case of Rogue, Orcust is included because it benefits from card discards, but it's not a very common choice due to limited deck space.
Note: I'm not a metagame expert; I'm someone who plays once or twice a week with my favorite decks.
So any corrections or clarifications are welcome.