Sadly I didn't finish my collection... YET. One day dammit.
A great thing about Japan is that if you have a hobby, there is a store dedicated to it. Hell there might be a dedicated block to just one thing. Pokemon cards are no different. There's a ton of dedicated trading card shops, and you can also find cards at recycle and used good shops.
Now most trading card shops only have new stuff. It's the nature of the trading card business. Many places have old cards, but just a random assortment. For Pokemon cards, there are cards known as 旧裏面 or "old card backs". These were the card backs for the Gen I-II cards before they switched to a design they still use today. Base - Rocket, which I was collecting, all have this card back.
Some card game shops have a little section for 旧裏面 cards that is a completely random assortment. You might even have to ask the clerk if they have them. At the store where I bought my Charizard card (plus several others), they were hidden behind the counter in a binder that they let me flip through. Other times they are out in the open, but in a cardboard box that you have to flip through. It's likely that the majority of the 旧裏面 cards are actually from Gen II because I'm sure a lot of collectors snatched up the Gen I cards, but I was still impressed at how many cards I just picked out by hand from a store.
I got a lot of these from a store called BIGMAGIC in Ikebukuro which I recommend. I don't know what their old card stock is like now, but when I went I felt like I hit the jackpot. They also have some rare cards on display that are fun to look at.
Probably the best Pokemon card store in Tokyo is
Cherumo. It's very tiny, but they have a great selection and a lot of unusual and interesting items. Mostly new cards, but they do have quite a large selection of random old cards as well.
Surugaya's Trading card shop in Akiba also has a nice selection but the prices are a bit jacked up since it's aimed at tourists. LOOK AT THIS NONSENSE:
Though if you are going to buy Japanese cards, the best way to go is online like Yahoo Auctions. Prices might be wacky, but it's definitely a lot easier than store hopping and digging through countless cards just to find one you might buy. I doubt those stores get a fresh stock of old cards frequently, what they have is what they have. But it's still cool to just walk into a store and hey, here's a bunch of 20 year old trading cards just sitting in a box.
[edit] I realized I never answered the question about prices. Common cards can be cheap, like 100 JPY. Even holographics only set me back maybe 200-700 JPY each. Though I am not a real stickler, as long as it isn't completely scratched up and there's some shine still on it I'll buy it. Online can be all over the place, though you can get good deals if you buy bundles or sets instead of individual cards.