Personally I've always preferred Takahata's work over Miyazaki's (whose output is still world class...). Only Yesterday is severely underrated in my opinion.
Fortunately, one doesn't have to choose! I love both Miyazaki's and Takahata's work. Recently (?) there was an influx of Ghibli movies on Netflix, so I finally watched "Only Yesterday" and... I loved it! I strongly recommend this movie.
Of course there's also his powerful "Grave of the Fireflies", but I think that one is well known by all anime fans and needs no recommending.
Don’t confuse “relatively unknown” with “underrated”. It is very highly rated: “The film received widespread critical acclaim. On Rotten Tomatoes, the film has a rating of 100%”.
