Nothing wrong with Fuji, I love it..though I generally like technical tracks. I used to hate Fuji, like a lot of people do. But after spending some serious time on GT5P practicing and testing setups as well as racing competitively, it grew on me.
The corner combinations create some great racing, pretty much you can do switchback-overtakes the entire lap because there are so many different lines you can take and different cars and drivetrains gain advantages in different parts of the track.
And contrary to what is said up there^ I think I've heard some F1 drivers speak favourably of Fuji in the past, I know Lewis Hamilton enjoyed his 2007 race there.
I personally think people tend to hate Fuji simply because they haven't raced it much..the same as Suzuka. They find it difficult to drive fast and make minimal mistakes and rather than attempt to grasp the challenge and practice, they rather give-up in frustration. It helps to have a little forced-practice by taking part in a competitive event at tracks like this, most of the time you can be surprised how much you can like a track if you just spend the time practicing.
Anyone who actively took part in the online racing a couple of years ago on GT5 Prologue would understand the enjoyment that can be found from both Suzuka and Fuji.
To answer the OP more directly though - overtaking isn't everything. Fuji isn't a great track just because it has a giant straight for overtaking on. You completely miss the point about what makes tracks fun. Suzuka is a better track because it has more interesting and flowing corners, it doesn't matter that overtaking is more difficult, the track itself is much more enjoyable to drive on and the challenge is more appreciatable than the wide, sweeping Fuji layout.
We could have circuits that comprise of two straights and two corners that would produce loads of overtaking - does that make them the best tracks? No. So why do you think Fuji is a better track just because overtaking is easier? Is the Daytona Oval the best track then? A circuit isn't defined simply by how much overtaking it produces, its just one of many attributes that can make circuits great.