Depends how you use them.
Meganium is a great Psuedopasser(Passes Reflect and Light Screen), while Sceptile is owning the grass world in RSFRLG(Leech Seed, something, something, and something eats you). Meganium is practically NU(Never Used) compared to the OU(Overused) Sceptile.
Thus, I pick Sceptile, it's going to be the next Alakazam: Only stronger.
EDIT: I forgot to add look-wise comments.
If I'm going by looks, Sceptile DIES and Meganium rises from the dead. I mean, wat the yams, Sceptile is a gigantic plant lizard with some gigantic balls on its back, while Meganium is a beautiful Dinosaur with colourful petals surrounding its neck. Duh.