Now that I've finished the game, I will restart with some eggs, so I'll ditch them again. Guess they are really ditchable. Samurott is probably the best one since water types are good. Darmanitan/Volcarona outclasses Emboar quite easily, with early access to the monkey-ball-thing. Simisear is quite better as a mixed sweeper in-game thanks to higher speed. Virizion outclasses Serperior, though if you don't like using legends, like me, you might use Ferrothorn or Simisage. If you want to go special there's Roserade, my favorite pokémon, pretty destructive in story mode.
Even Samurott is easily replaced for something better, though later than the others, if you do not want using a Simipour.