Ok, so I can't give full-detailed explanations for all, since I've barely played Gen V for example. However, I will give it my best shot:
Kanto: I would say that Saffron City would most likely be the capital city. It has a very many business corporations situated there, plus the monorail, and Silph Co. would only really be based in the capital right, as such a large company.
Now onto more real-life points. Saffron City is situated at a crossroads. Think about how towns and cities built up in history, they start as one person selling wares at a significant through-pass for traders and merchants. With towns north south east and west of it, it's not hard to think that the area would have had a lot of traders travelling through the area. This means it will have had access to more trade than any of the other cities would, as not all traders would go to all, but all WOULD pass through the Saffron area. Hence it would also have built up a lot of money, to become Kanto's biggest city, and capital.
Johto: This is irrefutably Goldenrod City. The only city in Johto that has even a hint of a commercial and developed background. It's location doesn't lead to the same argument as for Saffron, but location doesn't mean everything. Since Goldenrod is so significantly built up to the point of outshining any other city in the region, the area must have been a significant travel route for all traders in the area. Perhaps due to the route or because of the constant blockages thanks to Sudowoodo, either way Goldenrod became immensely successful, also gaining Johto's part of the monorail, and the Radio Tower. I think it is safe to conclude Goldenrod as Johto's capital.
Hoenn: Many of you have said that Slateport or Rustboro would be Hoenn's capital, however, I would ague different and say that Mauvile is Hoenn's capital. Even before the remakes, it was clear that Mauvile was an immensely rich area, with it's 'Mayor', Watson, having also developed New Mauvile, in the hopes to make Mauvile a more sustainable city. Also, again, it's location just makes sense! It is also at a crossroads, receiving trade from all directions. It also has the Game Corner, an extremely expensive luxury entertainment center. Rydell has also set up his Bike store there, in the hopes of getting his name known. Where would you set up a new store in hopes of getting your brand known? The capital of course, where the majority of trade flows through and people from all over witness your brand. The remakes only solidify this idea, with Mauvile become even more of a wealthy city, sharing development ideas with Lumiose city (Kalos's capital, without a doubt). So for Hoenn, I give you Mauvile as the capital.
Sinnoh: This one is between Hearthome and Jubilife. One the one hand, Hearthome is incredibly weathy, popular and brings in a lot of outsiders for Pokémon Contests. It is also slap bang in the middle of Sinnoh, providing a rest point for travellers coming through the mountain, and about to go through. That said, Jubilife is connected on three sides to travel routes to other cities, including Canalave which means that Jubilife is in close vicinity to many other region's trade as well. I think my final conclusion for Sinnoh, would be Jubilife, simply because of its connections and commerce over Hearthome.
Unova: There's no reason capital cities shouldn't be next to the sea as ports too, they often just aren't, as trade often doesn't stop at the port upon import, and exports aren't suddenly going to be sold to companies on the coast. It's not a economically sounds area to settle a business in. This makes me question why Castelia city has so many tower blocks there. I'm unsure what companies could do there, over Nimbasa City, which would be my ideal choice for a capital city, based on location, and commerce, tourism and so on. I feel that Nimbasa City just fits the bill more-so than Castelia City, and it also feels a tad bigger, despite the fact that it isn't. That's all I can say really, I don't remember too much from Gen V.
Kalos. Does this one even need explaining after my previous explanations and just everything about it? It is clearly Kalos's capital. Without a doubt.
So that's my two cents on the topic. Hopefully it made sense :P
