There is no true best Skell since all of them can be customized to handle everything the game throws at them. I won't talk about all of them but I will go over the two most common ones. Both of which have one thing in common, they're easy.

The Ares 90 is a high floor and low ceiling Skell. It's stupidly strong out of the box and doesn't require as much work as the others, but it's limited in what it can do. It is bad at farming most augments due to it not being able to equip M-Missiles and the two non Ether arts suck.

The Lailah is in a similar boat. It doesn't take much to make it so that it can defeat most enemies in the game. It's damage is one of the worst if not the worst out of all the Skells. (I'm not sure if the Formula is weaker since it does get crit rate up with it's Overdrive but crits don't do that much in this game.)