Final Smashes aside, characters themselves have different strengths and weaknesses. Getting smashed by Pichu is very different from getting smashed by, say, Bowser. Of course Pichu's weakness is made up for by his speed, and while Bowser is strong, he is much slower than the other brawlers.
Likewise, Samus' Final Smash might look strong, but once her smash begins, she can't move around, making her attack easier to dodge. Diddy Kong's Final Smash might look weaker, but he has the freedom to fly around and choose where to attack.