My average game came out in 2003.24 (so WindWaker's US release date is almost at the dead chronological median for me)
The 50 clues:
50. Came out this year, the first entry in its franchise in 21 years (Kid Icarus: Uprising)
49. The only game in this franchise where the flagpole yields coins and not points (Not guessed!)
48. These games are deceptively titled, as they have monochromatic titles but are in color, compared to earlier colorful titles of monochromatic games (Pokemon Black and White)
47. This game is a ripoff of Final Fantasy in name but not in gameplay (The Last Story)
46. A gang of four animals on a quest to take out a monkey (not guessed!)
45. The protagonist of this game could be called "Star Wolf." (Okami)
44. 6th gen launch game. It's franchise's first foray into 3D. Controversial cat stages (Sonic Adventure)
43. This game existed alongside the PlayStation2, and shared it's acronym. (Pokemon Stadium 2)
42. This is the second time this game, direct sequel to one of the most recognized games of all time, made its way overseas (Super Mario Bros DX)
41. Double the fun (Mario Kart: Double Dash!)
40. The second time this publisher made a "Dark" version of one of it's characters (Metroid Prime 2: Echoes)
39. The name was changed midway through development to reflect its developer's legacy (Xenoblade Chronicles)
38. This being the second made by F5, this game covered entries 4, 5, and 6 and the events in between (not guessed!)
37. This game's "Story Mode" deserves to be called such. Features stages such as Frustration, Shy Guy Limbo, and Jelly Pipe (not guessed!)
36. A direct sequel in a franchise that rarely gets them, based on deleted content from the previous game (Super Mario Galaxy 2)
35. Ritzy-titled games that brought online features to their franchise (not guessed!)
34. This game featured swordfights, a dog, cycling, and a hidden watermelon (Wii Sports Resort)
33. The boxart of this game featured the title character holding up three fingers, both for the entry in the franchise and the character's name. (Wario Land 3)
32. Herpes (No More Heroes)
31. Boom 2^6 (Bomberman 64)
30. This game, one of the best-sellers of the last generation, helped sell a piece of functionless plastic (not guessed!)
29. The protagonist of my number one game makes her only 5th-generation appearance here (Super Smash Bros).
28. The first time this franchise went simultaneous multiplat, one if its publisher's first works as a 3rd party (Sonic Heroes)
27. The protagonist is infected, but that only makes her stronger (Metroid Prime 3: Corruption)
26. A little water solves all your problems (not guessed!)
25. A lot of water makes for an apocalyptic backstory (Legend of Zelda: Wind Waker)
24. Monochromatic games with a colorful title (Pokemon Red/Blue)
23. It was too easy, Alec (not guessed!)
22. Protagonist pony + Female royal heir (Zelda: Twilight Princess)
21. You can be anything! Darth Maul, a refrigerator, a dynamite miner, or fireworks! (not guessed!)
20. Early FUD about this game spread the idea that it was just a DS port (New Super Mario Bros Wii)
19. This game fulfilled the promise of its console and served as a prequel for the entire franchise (Zelda: Skyward Sword)
18. Hype was built for this game by a blog (Super Smash Bros Brawl)
17. The first area of this game served as the subtitle for the game's sequel (Super Mario World)
16. 10 years before the specific game that spawned "Red vs Blue" was another game that could also have this description, with the bonus of fusion power (Sonic and Knuckles)
15. Sales of this game were so disappointing that the franchise went dormant for 8 years (Super Metroid)
14. The franchise started on consoles, got famous on handhelds, then with this game, jumped ship to a new manufacturer who promoted it in the West (Monster Hunter Tri)
13. Damn this rainbow is long (Mario Kart 64)
12. 9th in its franchise, but the first to appear on a console worldwide (not guessed!)
11. Subtract 10, and you get where this game usually is (Zelda: Ocarina of Time)
10. This game had enough cut from it to build a sequel around, but it was still great despite the cut content (Super Mario Galaxy)
9. You'll get no medals for guessing these games, who introduced a lot of big features to their franchise (not guessed!)
8. Introduced a purple-clad character who is hated for reasons i never quite understood (Mario Tennis)
7. You couldn't get hurt by enemies, and one ending of the game could only be gotten by doing absolutely nothing at the very beginning of the first stage (Wario Land 2)
6. Three epic sub-stories. Didn't use its console's main feature at all. Showdown with a Goddess. (not guessed!)
5. Dinosaur on the roof (Super Mario 64)
4. Basically the only online game on one of its platforms, direct sequel to the first major console online game (Phantasy Star Online Episode I & II)
3. This game was infamous for a certain type of player who liked to play on only on a stage named after a fate-based horror movie series (Super Smash Bros Melee)
2. Introduced a character who was beloved at the time, but hated just four years later when he got his own game (Sonic Adventure 2)
1. It's a 1, 3, 5, 7, 11, 13 kind of parasite (Metroid Prime)