Yes. Every time, actually, except for in platinum. I loved my Empoloeon too much for that. --- They have tried to rid this site of me BUT I'LL ALWAYS BE BACK! Bi and proud. http://www.youtube.com/watch?v=qcu_Yb7gwL8
I never have in my main playthroughs. The most you can really consider as "boxing my starter during the storyline" was for my Rotom-only run in SoulSilver. --- "The Underworld Army is here to steal magma!" - Pit Official Zorua of the Pokemon X / Y boards.