There's even a clear example of this in the non-legendary teams: both of them include Slaking, presumably because it has a particularly high base stat total (the highest of any non-legendary, and matching some legendaries).

But Slaking doesn't get that for free-- it has an ability (Truant) that means it can only use moves every other turn. That limits its usefulness outside of a couple very specific scenarios, and means that it'll usually be outperformed by significantly "weaker" Pokemon (going purely by numbers).

And that's just one of the factors you'd need to take into account to build a team optimizer that's actually useful. Actually building a team has to take into account a massive number of factors: roles for each Pokemon (not just what types they can counter), available movesets, any advantages or disadvantages provided by abilities, your opponents' team composition, etc... it's a big problem to try to solve.