This thread is naturally going to get resistance. You're describing a period of gaming in which people came of age. For many younger people, playing Modern Warfare or Mass Effect on Xbox 360 is their "classic arcade", "16-bit console war" or "PS2 era", or whatever your personal gaming golden age is. And I'm not saying it's all youthful nostalgia. If your vision of gaming is deathmatching FPS games with your buddies through party chat online, I'm sure it was a dream.
But I don't think the OP is that wrong in that for a lot of us older/colorful-fantasy-game-loving/Japanese-game-raised types, it was broadly a down period in gaming history. And with the recent resurgence of these types of games on PS4, the late 2000s feels like the odd era out for our tastes.
And also..... no one on earth likes fucking VGcats.
2004-2007 were pretty damn good if you were into colorful Japanese games. Those were the years when the PS2 hit its stride, the Wii launched strong out of the gate, the DS and PSP started really taking off, and MS was actively courting JP devs, so amazing Japanese games were all over the place.
2004 - Gradius V, Katamari Damacy, Shadow Hearts: Covenant, SMT Nocturne, Tales of Symphonia, Ninja Gaiden, Viewtiful Joe, MGS3
2005 - Dragon Quest 8 (best PS2 game for me), Lumines, Digital Devil Saga (another PS2 favorite), Kirby: Canvas Curse, Radiata Stories, Gunstar Super Heroes, Mario Kart DS, Ys 6 (PS2)
2006 - Suikoden 5, Wild Arms 4, Kingdom Hearts 2, Mother 3 (best GBA game for me), Baten Kaitos: Origins, God Hand, Valkyrie Profile 2, FF5 and 6 Advance, Outrun 2006, Twilight Princess. It wasn't that great in hindsight but New SMB revitalized 2D platformers for a while.
2007 - Gurumin, Kororinpa, Wild Arms 5, Persona 3, Every Extend Extra, Mario Galaxy, Virtua Fighter 5, Blue Dragon
Now after 2008, when MS realized Japan was a lost cause for them and pivoted to supporting Kinect, when the western press got increasingly xenophobic, when Japanese games tried to copy what was popular in America, compromising the things that make them so unique, when it seemed like every other game was a set-piece based first or third person shooter with ugly-ass brown and grey, when several popular Japanese games almost slipped through our hands (Operation Rainfall being the most notable) that was the dark ages. Looks like over the last 2 years we are finally getting away from that, 2017 is on track to being the best year for me in gaming since like... 2001.
I think my worst years were probably 2009, 2011, and 2013. Can't remember enjoying too much during those years.