Last week, I took a trip to Shikoku for sightseeing and roller coasters. The island has a four-team independent league but I wasn't able to catch any games. It seems that there are three card shops in Shikoku, and I was able to visit two.
The first was a pretty successful visit. Hot Box!? (yes, with the exclamation point and question mark) is just north of the tourist attractions, one short block from a tram stop. It's a smaller store in size. Note that I say successful, but by that I mean I found the shop and it carries trading cards.
However, I don't think you should go out of your way to find singles at this shop; Matsuyama is out of the way for most tourists and I would expect that everything here can be found at other shops.
Hot Box!? also carries packs and boxes of current product; I saw Donruss Series 2 already on the shelf (420 yen [$4.20]/pack). There are some figurines and gaming cards here, in addition to J-League soccer, some NBA, wrestling, and other sports.
And in one corner of the store, right next to the door, were several snacks. I get the feeling this store is frequently visited by school kids on their way home, due to the stock they carry (other than idol cards, of course).
Prices for singles start at 50 yen each. Note that they charged me sales tax on the singles I bought. This is the only store so far where I've had this experience. NPB packs are comparably priced to other stores - perhaps a little on the high end - but the MLB packs seemed higher than other stores.
The shop is open 11:00-20:00, closed Tuesdays. The guy working when I visited understood very simple English at best though he tried to be helpful.
Overall, I was happy with my experience here, as service was friendly and it's a small shop; however keep in mind that selection is limited to the major issues and prices are average to high. If you're living in or visiting Shikoku, this might be your only outlet for trading cards. But while there might be a hidden gem here, I don't think it's worth going out of the way for.