In season 1, he's supposedly the (second) strongest person on Earth, and yet still gets routinely beaten to a pulp by just about everyone, including some random beastman guy. Nobody can even really put a scratch on his father. Makes it clear Earth is pretty much defenseless.
In season 2, we learn that a lot of what he is lacking is actually mostly technique rather than raw strength. He can defeat some of the weaker viltrumites, but not really yet, usually. We also learn that there are a lot of things in the universe that are stronger than they are (from those books).
In season 3, he's explicitly stated to have trained to become much stronger and faster. He is able to, at the very least, give the strongest viltrumite a good fight, and defeat him with help. Even the beast guy who almost killed him so easily in season 1 turns out to actually have been strong enough to fight any viltrumite all along, so losing to him was actually to be expected.
At the same time, he spends most of the season getting almost killed by everyone again, but mostly by things and people from Earth. Additionally, several of his weaker alternate universe versions were also handled without his help. We also learn that a "full" invasion will only be a couple dozen people at most. So now we know that Earth isn't actually defenseless at all anymore.
I think that's where they were going with it?
That being said, the episode with the giant bugs didn't handle any of this well.
I mean, seriously... 
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