Let's look at the pokemon that have been argued to be a threat against the lions and why their power is overstated.
>Magcargo
The biggest defense of the Pokemon side is that Magcargo is so hot that it would instantly vaporize the lions and the resulting carbon of one billion lions simply isn't enough to smother magcargo enough to neutralize it
However, even with Magcargo taken into consideration, one billion lions would still beat one of every Pokemon.
If we assume the Pokedex is right with respect to Magcargo, and the fight is taking place on an environment that wouldn't instantly collapse due to the existence of Magcargo, then it's true the lions wouldn't be able to get close to it, but - and this is important - neither would the Pokemon. Magcargo would have to be so far apart from both Pokemon and the lions that it basically isn't even part of the equation anymore No pokemon is able to reach the magcargo in order to support it.
There are no other pokemon that threaten one billion lions as much as magcargo, so if the lions can kill every Pokemon, all they'd have to do is starve Magcargo and the lions will win.
>Jirachi
You could argue, can't the pokemon just wish for Jirachi to wipe out all the lions?
The answer is no, because nowhere is it stated in the Pokedex that Jirachi actually CAN grant wishes. It's just a legend.
>Arceus
Couldn't Arceus will the lions out of existence?
No, because Arceus' power is limited, evidenced by the fact that it can be taken out by other Pokemon. While the dex states Arceus is only rumored to be this deity like figure, we actually have canon events of Arceus performing crazy shit ie the egg event. So it's not the same as Jirachi where there isn't any canonical evidence that Jirachi can grant wishes. Still, there is no canon that Arceus is able to will things out of existence, so we can't give this ability to arceus. We know it can create life, but nothing more can be assumed