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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.
I'd actually prefer if they just kept it all separate, add a new Cafe' building. where i can get my hourly injection of Caffeine. and that would make the Outposts they call "Cities" seem even bigger.
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.
It's not just a matter of convenient but also that a separate mart building fills town space in older games where they couldn't do things like the 3D crane in Virbank City for instance.
I say connect them. From a pragmatic POV, I like not needing to keep track of both buildings' location at all times, especially in ROM hacks where some cities are huge.
It'd be fine if the city designer just kept them close to each other at all times, but that's not always the case.
I'm all for it. You could make the mart the second floor or something. I mean it's not like we can connect with another rom/emu player right?
Plus you can use the mart building for something else. I had the idea of turning the mart into a maniac/hobby shop where you could find and buy rare items and offering up other services. Or even trade items that are common in area but rare in another. Like berries.