I understand that placing Pokémarts inside Pokémon Centers was done in later generations and to be fair having the two combined is more convenient for the player. Even with that considered, I personally like having standalone Pokémarts still. Makes towns and cities feel a little bit bigger with the extra building.
It's a question of convenience. Marts in Center (much like say, having Jack do Move Reminder + Move Deleter + Nickname Rater in the center) is convenient to the player and has less backtracking and wandering to do in big maps.
On the other hand, I suppose it's a bad thing if you care about having big immersive maps. Personally, I'd keep Marts in Center and use the space for something else - maybe a minigame, maybe a quiz. Marts take up space but they don't really do anything exciting, so in a way they make the map have less usable space.