I wasn't aware that the first couple regions were based on parts of Japan. That changes my perspective. Though we can't really be sure if the size of those regions are the same size as the places they're based on relative to the size of the planet. Then there's the issue of just how big the Pokemon planet is. Has there even been a good, accurate view to judge?
Somebody else said it really well, but honestly, how long does it take you to walk across town (the nearest town, if you don't live in one)? And then imagine that your town might not even appear as a dot on a map. The world is huge.
And because you asked, here is Unova in relation to the rest of the world:
Does it look like we're running out of space? Although, to be honest, I wouldn't take these maps too seriously anyway. Gamefreak has literally taken parts of the real world and stuck them on Planet Pokemon because they were too lazy to design new landmasses for areas that we have never even seen, on other maps and I know that as they add new regions they will add on brand new landmasses and pretend they were always there, if they have to.
Bulbapedia even says "Note the obvious similarities to Europe at the bottom of the picture; Scandinavia looks practically unchanged". I don't actually see it, but I have noted it in other maps, though I haven't been able to find them via Google in order to post them here.
Anyway, here is another picture of Planet Pokemon:
Looks similar to Earth, doesn't it? This has been this way for quite a while.
As a little side note, although I'm not sure how relevant it is, several real world countries have been mentioned within Pokemon canon, since the beginning of the franchise. For example, China is mentioned in Parasect's Stadium Pokedex entry from Generation I. Although it is true Generation I has tons of quirks that have never been seen again, and you might think "but Stadium is just a side game", this was once again mentioned in Pokemon Firered, a more recent mainstream game, and was in fact reworded which proves that the localizers (at least, maybe the original Japanese Pokedex entry writer(s) too) didn't just copy + paste (or they re-translated the Stadium entry, or something). There are a couple other examples, as well.
I'm just going to quote Bulbapedia real quick:
Arcanine's Pokédex entry states that it is considered legendary in China; in the anime, Jessie's mother was said to have been lost in an expedition in the Andes; and lab reports in Pokémon Mansion state that Mew was discovered in Guyana, South America. These observations imply some possibility of the Pokémon world being the same as the "real world", only with extra regions.
So, maybe that helps you ponder about the size comparison between regions on Pokemon and on Earth...?