The best ending is from WA3 because after taking down the Christmas Planet Weed, everything seems fine until other people finally show up and see their leader, dead, because the main villain and mother of the Planet Weed killed him earlier, but they just show up and assume you did it and try to kill you. Protags are very nice though, so they drop their ammo and make their escape without hurting anyone and long story.
You end up wanted criminals accused of killing a religious leader and no one will ever know you saved the world, so the team ends up staying together, on the lamb, but still helping save people when they can and
Okay it's not the best ending I just wanted to mention the final boss is fucking Christmas tree looking sentient weed thing at the core of the planet