Your opinions certainly are much different than my own. I loved the atmosphere in Metroid Prime. In fact, I found Metroid Prime 3 to be my least favorite (although still very good) in the trilogy, and a large part of it was because of the fact that they added more characters to the game. It was hard for me to get used to interacting with other NPCs in a Metroid game.

And as for the newer DKC games, have you played them, and if so, how much did you enjoy them? I found the new DKC games to be perhaps the best side-scroller platformers of the generation (at least I can't think of anything better off the top of my head). The amount of detail that goes into each and every level is astounding. Every single level seems to have it's own unique mechanic, and everything is animated so perfectly. And I found the controls to be among the best in the series; I loved the different playstyles of the Kongs, and the game never felt unfair, despite being difficult.

I'm very fond of the work Retro has done.

I always find it funny when people bring up Sunshine being rushed without mentioning the horrifically buggy pachinko game...
In addition to the Triforce fetch quest and simply being vine the pearl in Wind Waker, I always felt that the boss rush in Ganon's castle was there for no other reason than to pad the game...
Despite the GameCube being a flop, it still Gabe us some major moments...
Both of the Prime games were a moment, Pikmin is a gem, Thiusand Year Door was incredible, F-Zero GX is one of my all time favorite games, and Eternal Darkness is an unpolished cult classic for the ages...

But which parts of my post are you actually disagreeing with? If you're favourite platformers of the generation are the DKC revival games, my post isn't arguing against you for having that opinion, it isn't about that.

There were some great exclusives for the system, as well. Some of my favorites:

Lost Kingdoms (both I and II)

Baten Kaitos

Final Fantasy Crystal Chronicles

Resident Evil games (Zero, REmake, and RE4)

Viewtiful Joe

Now that I think of it, Capcom was really great with Nintendo in these days. They even helped with many of the handheld Zelda games (Oracle of Ages/Seasons and Minish Cap being the ones I know).

I'd heavily disagree with this sentiment. I think the Gamecube is the best Nintendo console ever made. The games that were on the console were great introductions to new IPs or were some of the best in the entire franchise:

-Super Mario Sunshine
-Windwaker
-Luigi's Mansion
-Geist
-Eternal Darkness
-F Zero GX
-Metroid Prime
-Resident Evil 4
-Smash Bros Melee
-Mario Kart Double Dash
-Pikmin
-Animal Crossing
-Paper Mario: The Thousand Year Door
-Super Monkey Ball
-Metal Gear Solid: The Twin Snakes
-Chibi Robo
-Kirby's Air Ride

Such a great variety of games that I don't think later consoles have been able to replicate.

Is Retro overrated? Maybe? Probably... They don't exactly have a big resume, so there are perhaps other devs more deserving of the praise. I certainly look forward to seeing what they have to offer, and I have enjoyed all of their major releases since they've been in business. HOWEVER... Metroid Prime is absolutely the only reason they get so much hype, and I freaking love the MP games.

The core of your argument seems to discredit them for their work on MP because the devs are no longer with the company. With this, I ask you: Is Star Wars overrated? Since Star Wars was sold to Disney, does that mean that we should no longer get hyped for SW movies? I'm having mixed thoughts on this.

People are really taking this the wrong way. I'm not saying the Gamecube was bad or that it lacked great games. It is by far the console I have the most nostalgia for, and I have never regretted getting it instead of the PS2 or XBox. I would never have gotten any Nintendo systems afterwards if I disliked the Gamecube, and I liked the system enough to become a lifelong Nintendo fan. I'm just observing a phenomenon that seemed to affect certain big first party franchises during that generation.

Rogue Leader is my favorite Gamecube game. I enjoyed plenty of titles like Super Monkey Ball 2, Melee, ect. Wind Waker is a great game even with its faults. Sunshine is good and has plenty of fun stages despite the frustration it can sometimes cause. Mario Party 4 was addictive.

I did have a tendency to get licensed games over first party titles back then, since I didn't know any better. But Two Towers, a bunch of Star Wars games, Ultimate Spider-Man, Batman Begins were all good.

Prince of Persia Sands of Time, Eternal Darkness, the Resident Evil games, Viewtiful Joe, there was a lot to love back then.

Pikmin 1 was rushed too. You could beat that game in ten hours.

In retrospect Gamecube is my favorite Nintendo Console. It got the most 3rd party support, and had the most quality exclusives out of NES, SNES, GameCube, Wii and Wii U.

Switch continues to get amazing support both from 3rd party and Nintendo though, so it may just surpass GameCube.

I certainly got that feeling from some of the Mario Party games, particularly Mario Party 4.

Glitching through walls doesn't count. 

And Pikmin 1 had days on timers so you were forced to either finish the game in a set amount of time, or lose. Technically, if you never repeated a single day you could beat Pikmin 1 in 6.5 hours, because there are 30 days lasting 13 minutes. But even if you went back and repeated multiple days via save scumming you still wouldn't be able to spend more than 10 hours on a single playthrough.