Quilava, for sure. With Espeon as a close second (though Espeon isn't part of a three-stage evolution line).
I agree. The poor second-stage Pokemon hardly get any glory, especially if they're the second in a set of three Pokemon. Their basic stages are loved for their cuteness, and the final stages are loved because they're powerful and awesome. The middle stages seem like nothing but a transition stage between the cute, adorable stage and the powerful, awesome stage. Me, though... I tend to get really attached to the middle stage, especially with starter Pokemon.
I could also stretch it a little and say Pikachu. Pikachu is technically a second-stage Pokemon (having spawned a pre-evolved form in the Johto generation), but it still feels like a basic Pokemon, having originally started out as one. Pokemon like Pikachu, Jigglypuff and Clefairy don't seem to get the same sort of second-stage neglect as Pokemon like Gloom and Weepinbell, who started out as second-stage Pokemon and have always been second-stage Pokemon.
