Now, I can't argue with the rest of that list, but that in particular will be a very contraversial decision...

Also, note that you've put it in your "crap" 3. The thread title says "Crap or overrated", so that's a little better, but you're trying to say that Skyrim is amongst the worst three games of the generaation doesn't add up. 

For the record I love Skyrim; recently "got" back into it on PC having played it before on PS3. Excellent title if you ask me.

My list, top 3:

Xenoblade

Galaxy 2

R&C: Crack in Time

Bottom 3:

Resi6

FF XIII

Assassin's Creed III

Top:
Mario Kart Wii
Super Mario Galaxy
Legend of Zelda: Twilight Princess
Overrated:
Legend of Zelda: Skyward Sword
Kirby: Epic Yarn
Zack and Wiki

Top 3:

Grand Theft Auto IV
Grand Theft Auto V
Red Dead Redemption

Most Disappointing 3:

Assassin's Creed III
Gran Turismo 5
Red Faction: Guerrilla

"Mass effect 1: The citadel. The first hours."

Having only played ME1 through the citadel and the first hours, I have to say, I think it would be closer to my bottom 3 than top three. The citadel was meaninglessly spread out and 99% of it felt the same, so I got to the point where I wanted to explore it but everything just looked the same.

Now, for my list...I will be choosing games that surprised me moreso than games that were just good/bad
Top Three:
-Demon Souls: I honestly didn't like this game the first time I played it. It was far too difficult and I couldn't really progress enough to get into it. However, upon returning with a new class (the magic class whatever it is called) I found the game much easier and it was a blast to get through. While the Valley of Defilement sucked, the game was one of my favorite games of last gen.
-Monster Hunter tri: I purchased this game after playing the demo (a wii game with a demo? insanity!) and I was hooked. I'm pretty sure this game holds the record for most consecutive days with over 5hours played. This game was my life for a few months in which I played it a ridiculous amount. Because of this game, I will forever call myself a fan of MH
-Legend of Zelda: Skyward Sword: Many people disliked this game and I can understand it, but for me it was more than amazing. The controls, the art style, the characters, the story...I will say, so far, this is the only game to ever make me cry (twice). For that it is worth a place on my list.
Honorable Mentions: Valkyria Chronicles, Xenoblade, Super Smash Bros Brawl, Super Mario Galaxy

Bottom 3:
-Epic Mickey: Dear glob was this game not what I had expected. I knew it wasn't the greatest game going in but I figured I would enjoy it more than your average consumer because I typically enjoy games of this style. I was wrong. The thing that sticks out to me the most was the music. Not because it was good, but because it was so bland and lifeless it just sucked me out of the game. This was the only game that really made me say "dear goodness this music is terrible", and for it to be a Disney game is surprising.
-Ni No Kuni: While this game does a lot of things spectacularly, such as the presentation and the voice acting, the mechanics are just not good. Playing through the game, I repeatedly thought to myself "this could have been done so much better" from everything from the battle system to the overworld to the capture system...quite a letdown.
-Red Dead Redemption/Mass Effect 1/Rayman Origins: Hold on, hold on! I know that all three of these are "great games" and whatnot, but they didn't hook me. RDR because of its empty, boring world, ME1 because of its...errr, pretty much everything (although some of it may just take getting used to), and Rayman because it just didn't feel good as a platformer. I plan to return to all of these games eventually and give them another go but for now, they sit on my shelf, barely touched...

EDIT: To add to the discussion above, I would like to say that the Last Story is a good game but it cannot be compared with Xenoblade. Xenoblade is huge and open where Last Story is compact and linear. That does not make it bad, but it contains far less wonder than a game like Xenoblade..

It's quite possible for someone to find a highly rated game to be crap, Final Fantasy XIII for example.

I loved Skyrim, but found Oblivion to be crap and have next to no redeeming qualities.

I did, although I've always had a soft spot for over the top action games that don't take themselves seriously. MGR has a ton of flaws, to be sure; the camera spazzes out whenever you get close to a wall, the game does a pretty poor job of explaining how it's supposed to be played, the stealth is dodgy at best and the few points where the game tries to be semi-philisophical are supremely cheesy. That said, it's probably the most fun I've had with any game in the past generation, and there's something to be said for that. The combat's tight, runs at a smooth 60 FPS, and most importantly, you get to chuck a Metal Gear Ray into the air and then slice it up while some guy is going nuts in the background about the rules of nature.

Top 3:
-Ratchet and Clank: A Crack in Time: What can I say? It had the best story of any Ratchet and was an outright tear jerker at times. The clock puzzles were great and the writing was simply fantastic as it had me rolling when I read something as simple as a weapon description or statue plaque. That shows true dedication by devs to fill every corner with character. The platforming and weapons were as great as ever and the RYNO V was simply my favorite weapon in the series.
-Uncharted 3: I liked it more than 2. There I said it. One of my most hyped games this gen and it did not disappoint. The set-pieces were the best in the series and from the first cutscene to the final boss I thought it outdid its predecessors in both production value and story.
-Puppeteer: Absolute charm around every corner. I could not put down this game and the whole atmosphere was pitch-perfect. I've never seen a game with so much character that outright bled with the passion of its devs.

Bottom 3:
-Demon's Souls: platinumed it but god damn it was horrible mechanically and taking away checkpoints to artificially extend the life of your game is NOT OK in my book
-Zelda Skyward Sword: This one is especially irksome because it COULD have been my favorite Zelda ever. I asked for it for Christmas (first Wii game in awhile and the last one I bought) and had my Wii motion plus ready, but GOD DAMN the controls were just horrendously crippling! The lag was waaaaay too much to be used in sword combat. I would stick my wii mote out to the right quickly and swing and Link would not even react to me! The wii-mote should have been used for aiming only. Not flying or swinging (or at least not that precisely but I guess they had to sell their peripheral). The final boss and dungeon puzzles were my favorite in any Zelda so far but it's not even close to my favorite overall because of these controller issues.
-Limbo: So much hype...so little satisfaction. I just didn't like the whole aesthetic or what it was trying to do. Once again I played all the way through but the puzzles never wowed me.

I'm about to play it soon too! Right after I finish up Ogre Battle 64.

TOP:

1. Xenoblade Chronicles (AWESOME! can't wait for X for Wii U)

2. Metroid Prime 3: Corruption (ok, I really like EVERY Metroid game)

3. Super Mario Galaxy

Crap/overrated:

1. Aliens: Colonial Marines

2. Sims 3

3. Resident Evil 6

Good

Platformer - Ratchet and Clank: Crack in Time (Honorable mentions to Little Big Planet, Sly Cooper 4 and Puppeteer)
Action - The Last of Us (Honorable mentions to Portal 2, Uncharted 2, Assassin's Creed: Brotherhood and Batman: Arkham Asylum)
RPG - Tales of Xillia (Honorable mentions to Ni No Kuni, Mass Effect, Final Fantasy XIII and Hyperdimension Neptunia)

Not so good or disappointing

1. Assassin's Creed III
2. Grand Theft Auto IV
3. Dragon Age II