I think part of the reason why so many people see squirrels as jokes is because a lot of the older squirrel cards were given a humorous treatment. Cards like "Acorn Harvest," "Nut Collector," and "Chatter of the Squirrel" just sound silly, even though there is nothing weird with them mechanically.

I think Squirrels lend themselves towards humor.Three squirrels walk into a bar… - 🐿

Creative had a problem with Deranged Hermit? If anything I feel like cards like Deranged Hermit and Nut Collector and friends do more to justify squirrels on the creative front than anything else. Squirrels didn't seem random or out of place because those cards were there in the first place, as it gave them some sort of tie in to characters that we can empathize with (being human).

One of the problems is that whatever is being played in tournaments gets the major amount of the focus. The creative team wants the spotlight to be on the center of the game and not the outskirts. Squirrels might have been fine if they were a cute thing way in the background, but having a spotlight shone on them made creative realize that anything they put in the game has to be something they’re willing for the spotlight to be on.  In many ways, Deranged Hermit was the death knell of squirrels.