Sazanamistyle: Oh boy. You've opened the floodgates. Prepare for the stupid negative joke posts about how somebody's an expert on an entire country's output of games because they've only played the minority that have been translated. This will especially be rich in terms of RPGs, where the generalizations are laughably untrue. But hey, ignorance about other countries is an eternal human constant, so what can I say?
If you want the best of Japanese games you can play in English, these days you're going to need a handheld, whether that's a tablet or phone, or the Vita/3DS or even the holder PSP/DS. Right now, for instance, there are all sorts of small Japanese games being sold digitally on the Vita and 3DS shops that absolutely compare to the rich originality of PC indie gaming.
Unfortunately, because as you state, there's a certain brain-dead follow the leader mentality going on in console gaming and a lot of console gamers seem to be caught up in that, not as many of the standouts get translated. For instance, there's still no confirmation of translation for the Yokai Watch games, which are utterly fantabulous RPGs about a kid who solves everyday problems in his town caused by mischief-making spirits. It's original, creative and innovative in all the ways a generation-defining masterpiece should be, but it has very little perception outside Japan. (That's 3DS, by the way.)
Since you're on GOG, though, you probably won't scoff too much at picking up a DS or PSP for old games, and there are more fantastic RPGs on those platforms than you could probably play in a lifetime. Also, because it seems like you might have an interest in old games, the 3DS' virtual console is great for that, but more than that M2 along with Sega has made the Sega 3D Classics one of the best reasons to own the 3DS. There are currently 11 games in the series and they are all faithfully recreated from old console and arcade classics, with awesome 3D quirks that replicate the TVs and arcade cabinets of those days. Wish you could have the experience of playing on old tube TVs with their curved monitors and scanlines again? There's an option for that. Wish you could emulate the experience of swerving left or right on an arcade cabinet complete with the squeaks of the hinges in the cabinet emulated? There's an option for that. Sonic, Bare Knuckle, Space Harrier, Outrun, Shinobi. It's utterly glorious and probably one of the greatest tributes to retro gaming the history of forever. Depending on how well a packaged version does in Japan this year, the collection may also continue to other games in the future too!
In short, portables and in particular the 3DS provide many of the peaks of Japanese-designed games these days, but you may have to have the Japanese version to get all the games you want and know a little Japanese to be able to play them.
Pardon me but no one here is actually claiming to be an expert, nor is anyone claiming seniority of opinion. It's all just opinions here, including yours. Are you trying to say that only a basement-dwelling weaboo or full-time hikikomori is allowed to have an opinion on Japanese games? Not even they have played or even know the majority of Japanese games, it would be quite impossible considering how many games that country makes every year.
There is a metric brickton of Japanese games available in English, more than anyone could finish in a lifetime unless you're a NEET and live to be 100 years old. I daresay that it's entirely possible to have an opinion on Japanese games even by judging only the ones that have been translated into English. It's true that some amazing gems have never been released outside Japan, my favorite example is Tobal No.2 which is still my favorite Beat em Up game despite it being 14 years old. But to suggest that the minority of translated games aren't enough to form an opinion on Japanese games isn't a convincing argument. According to Japanese friends & acquaintances, what we in the West get to play isn't the crap stuff but the cream of the crop - in general. That's what they say, not my words. Surely Japan has many cool indie gems that never see the light of the day outside Japan but you haven't shared with us any examples.
As for Youkai Watch being original...I'm not convinced that this "Pokemon with ghosts" is a good example for originality of Japanese games that aren't (yet) available in other languages. I haven't played it so this is only an impression but after watching some gameplay videos I truly don't see what is supposed to be so great about this.
If you could list some cool original indie games from Japan that are positively different from all the games that have been translated, I'd very much appreciate it.