Honestly, the first mon who came to mind was Chikorita. Sorry lil guy. It isn't personal. He has an attractive-looking evolutionary line, arguably the most consistent appeal of Johtos starters and tons of personality on the TV show. I just wish Game Freak put more thought into ways to use this guy, and not just how to make him cute.
The reason why I'd give him the boot is because he can't bring very much to the table as a starter. His final evo has no stat over 100 and he never received any buffs as the years went on, he has a forgettable movepool, no helpful hidden ability, no duo typing to support him as a defensive Pokemon. Most players will concedd that he's the worst of all 21 starter competively, and was dealt the worst possible hand in-game.
How would removing it change things? It would rip a hole in the fabric of time and space to do something as bold as take away a starter, definitely impact how you play the game. But I think it could also be an interesting opportunity to create a new, improved pokemon since his line isn't just going to be removed but can be replaced with an original grass type.
