3rd Gen 1000 Reasons Why...

1. Best Region Design ( Hoenn )
2. The Elite 4 are a actual Challenge ( Hoenn )
3. The Trick House
4. The 3rd Gen Pokemon
5. Rayquaza
6. The Story ( especially in Emerald )
7. Secret Bases
8. Re-matches through Vs.Seeker
9. The Underwater Dive mechanic
10. Steven Stone

1. Looking out of the porthole on the S.S. Tidal
2. Peeko
3. Better Dive spots than Gen. 5 :P
4. Dewford Town
5. Water type Leader and Champion
6. "Team Aqua was here!"
7. "Team Magma rules!"
8. Seaside Cycling Road
9. Oceanic Museum
10. Pacifidlog Town

1. Secret bases
2. Gym mazes
3. Full color!
4. Trumpets
5. Trick House
6. First generation to introduce remakes
7. Battle Frontier
8. Pokémon Contests
9. Outside-of-battle weather
10. Puddles/footprints!

1. Hoenn. Georgious region.
2. Weather.
3. Colosseum/XD.
4. The interaction between Gamecube, e-reader, GBA and even special RL items like the Eon ticket. All gens have this, but I found 3rd gen's to be fun, and clever.
5. Contests and berries! Hey, it's better the Musicals :P
6. VS seeker.
7. Double battles.
8. May and Brendan, aswell as Blue given life as Leaf!
9. First remakes!
10. Battle Frontier

1.Hoenn
2.Emerald's battle frontier
3. The Elite Four
4. Dat music
5. Trumpets in every song
6. The starters
7. Gardevoir
8. The fact that you can easily hack them
9. First gen I played
10. The starters

1. Rayquaza
2. Rayquaza
3. Rayquaza
4. Rayquaza
5. Rayquaza
6. Rayquaza
7. Rayquaza
8. Rayquaza
9. Kyogre
10. Rayquaza

But for cereals:

1. The lush variety in all the locales, from your more basic towns and cities to a village in a trees, a town floating on logs, and a CITY INSIDE A FREAKIN' VOLCANO.
2. The Braille puzzles to get the Regi trio.
3. The absolutely brilliant legendary design, still hands down the prettiest and most consistent of all the box trios out there.
4. Hoppin' around on mah Acro bike
5. Castform - never used it much, but I love the uniqueness
6. On that note, all the weather conditions, like raging desert winds and fierce rain.
7. All the new details, like water that reflected you, double battles, stuff like that.
8. My spirit Pokemon, Loudred.
9. The Battle Frontier.
10. MOTHERLOVIN' RAYQUAZA

1. Best tileset (RSE)
2. Best gym leader (Norman)
3. Best Pokémon (Flygon, Deoxys, Relicanth, Swampert, Slaking, Shedinja, Sceptile, Blaziken, and so much more)
4. Most fun victory road
5. Best environments
6. Most fun post-game
7. Best Battle Frontier
8. Best character design (Brendan)
9. Best girl character design (FRLG)
10. Best rivals (May/Brendan + Wally)

1 Awesome OST
2 Dive: treasure hunting and exploring ancient relics
3 Complicated designs of Legendaries
4 Hoenn Pokémon
5 Hoenn Contest
6 All important characters; villain, neutral or good ones
7 Desert close to volcano
8 Meteor Falls
9 Rain forest and tree houses
10 Abundant of water :D

1. Beautiful region
2. Legendary pokemon quests
3. Cycling roads
4. Battle Frontier
5. Sevii Islands
6. E4
7. Pokemon contest
8. Graphics
9. Good story lines
10. Prof oak, Brich

1. VS Seeker
2. Battle Frontier
3. Ballin' Legendaries [ Rayquaza, Moltres, Groundon, ... ]
4. My Shiny Goldeen
5. Safari Zone
6. Cool Starters [ Mudkip, Charmander, Squirtle, ... ]
7. Trick House
8. Contests
9. Sevii Islands
10. Fossilized Pokemon

1. The better coloured sprites
2. Tag Battles
3. Having Flamethrower, ThunderBolt and Ice Beam as TMs
4. Abandoned Ship
5. Learning Braille
6. Getting the guy to sing a song in the Mauville Pokémon Centre
7. PokéBlock
8. The HM Slave Pelipper
9. Move Relearner
10. Wynaut Egg

In no particular order:

1. Return to Kanto with improved graphics, more content, and less glitchiness
2. VS. Seeker in FR/LG
3. Battle Frontier (Emerald)
4. Mach bike was fast
5. Introduction of faster egg hatching via abilities (Emerald)
6. Elite Four getting stronger for second round/rematches (in some of the games)
7. Not strictly from the main handheld games, but I really enjoyed the concept of Colosseum and XD
8. No more saving every time you switch boxes
9. Running shoes
10. Return of Blastoise (my favorite Pokémon) as a starter