Thats not what I meant, I mean that sure, they are the same stat wise, but it has been shown numerous times that Pokemon have their own personalities. While I'm sure the two haven't been together for very long since its still Lv5, its would still hurt pretty hard if your starter pokemon, basically the equivalent of your first friend (not that your Pokemon is your first friend, its just a comparison), was taken away from you and the Gym Leader, the man you looked up to, didn't even try to get it back and instead gave you a new one. Even in the short time they were together, they must have at least bonded enough that the Pokemon actually listens to your commands and trusts you.
From a game standpoint, sure, its the same but from a real world (well Real Pokemon World) perspective, each Pokemon has its own distinct personality and features, they can't just be replaced, they are basically just small people that shoot fire/electricity/water/trees/rocks/the ground/darkness/faries/dragons/steel/ice/whatever
Also note that this isn't meant to be an insult to you, its just a harmless little Joke