OK, I'm just going to post a long list of my personal favourite stuff that has come out in the 2000s. There is probably way way more great music that I've never even heard. Briefly in answer to the thesis put across in the OP, the bands you've listed were the biggest bands of their time. This doesn't happen so much any more, mostly because of the way music is marketed to children. However, saying that there is no good music any more is simply idiotic. I'll go alphabetically through my collection and I'll choose just one album by each band:
Adem - Love and Other Planets
Aereogramme - Sleep and Release
Amen (ok, it's 1999 but it's great)
...and you Will Know Us By the Trail of Dead - Source Tags and Codes
Animal Collective - Strawberry Jam
Arcade Fire - Funeral
Arctic Monkeys - Whatever People Say I am That's What I'm Not
Asobi Seksu - Citrus
At the Drive-In - Relationship of Command
The Avalanches - Since I left You
Bat For Lashes - Two Suns
Battles - Mirrored
Beck - Sea Change
Belle & Sebastian - Dear Catastrophe Waitress
Ben Folds - Rockin the Suburbs
Ben Kweller - Sha Sha
Beth Gibbons - Out of Season
Biffy Clyro - Blackened Sky (or Puzzles if you're a populist)
Bjork - Vespertine
Black Keys - Brothers
Blackalicious - Blazing Arrows
Bloc Party - Silent Alarm
Blood Brothers - Burn Piano Island Burn
Bon Iver- For Emma, Forever Ago
Bright Eyes - Lifted
British Sea Power - The Decline of British Sea Power
Broken Social Scene - You Forgot it in People
The Bronx
Cat Power - You Are Free
Cave-In - Jupiter
City and Colour - Sometimes
Clutch - Pure Rock Fury
CocoRosie - Noah's Ark
Conor Oberst
Converge - Jane Doe
Cansei De Ser Sexy
Danger Doom - The Mouse and the Mask
Death Cab for Cutie - Plans
Death From Above 1979 - You're a Woman, I'm a machine
Deerhunter - Halcyon Digest
Deftones - White Pony
Desaparecidos - Read Music Speak Spanish
Desert Sessions 9&10
Devendra Banheart - Rejoicing in the Hands
Dillinger Escape Plan - Ire Works
Dimmu Borgir - Death Cult Armageddon
Dirty Projectors - Bitte Orca
Dizzee Rascal - Maths and English
Dntel - Dumb Luck
Doves - The Last Broadcast
Dwarves - Come Clean
Eels - Blinking Lights / Souljacker
80s Matchbox B-Line Disaster - Horse of the Dog
Emmy the Great - First Love
Everclear - Songs from an American Movie vol 1 and 2
Explosions in the Sky - How Strange, Innocence
Fall of Troy - Doppelganger
Fang Island
Fiest - the Reminder
Finch - Say Hello to Sunshine
Flaming Lips - Yoshimi Battles the Pink Robots
Fleet Foxes
Flight of the Conchords
Four Tet - Rounds
Frank Turner - Love Ire and Song
Freelance Whales - Weathervanes
Friendly Fires
Fugazi - The Arguement
Fujiya & Miyagi - Transparent Things
Future of the Left - Curses
Glassjaw - Worship and Tribute
Go! Team
Godspeed you Black Emperor - Raise your Skinny Fists...
Goldfrapp - Black Cherry
The Gossip - Standing in the Way of Control
Green Day - American Idiot
Grinderman
Groop Dogdrill - Every Six Seconds
Gutter Twins - Saturnalia
Head Automatica - Decadence
Health - Get Colour
Hell Is For Heroes - Neon Handshake
Hope of the States - Lost Riots
Hot Chip - Warning
Hundred Reasons - Ideas above Our Station
I'm From Barcelona - Let Me Introduce My Friends
I Come to Shanghai
Icarus Line - Mono
Interpol - Turn on the Bright Lights
Janelle Monae - Archandroid
Jenny Lewis - Rabbit Fur Coat
Jenny Owen Youngs - Batten the Hatches
Jetplane Landing - Zero for Conduct
Jimmy Eat Word - Futures
Joanna Newsom - Ys
Jonah Matranga - You're all these Things and Then You're none Vol 2
Jose Gonzalez - Veneer
Juliet and the Licks - ...Like a Bolt of Lightning
Justice - Cross
Kanye West - MBDTF
Klaxons - Myths of the Near Future
The Knife - Silent Shout
Kong - Snake Magnet
Kutiman - Thru You
Lamb of God - New American Gospel
LCD Soundsystem - Sound of Silver
Lightning Bolt - Hypermagic Mountain
Lightspeed Champion - Falling off the Lavender Bridge
Long Blondes - Someone to Drive You Home
Los Campesinos! - Hold on Now Youngster
M Ward - Post War
M83 - Dead Cities, Red Seas
Maps and Atlases - Perch Patchwork
Mark Lanegan - Bubblegum
Mars Volta - Deloused in the Comatorium
Martin Grech - Open Heart Zoo
Masters of Reality - Deep in the Hole
McClusky Do Dallas
Megachurch
Metric - Fantasies
Million Dead - Song to Ruin
Minus the Bear - Minos el Oso
Mogwai - Hardcore will Never Die but You Will
Mondo Generator - A Drug Problem that Never Existed
Monsters of Folk
Morningwood
Mum - Go Go Smear the Poison Ivy
Muse - Origin of Symmetry
My Chemical Romance - The Black Parade
NERD - In Search Of...
Naked and Famous - Passive Me Aggressive You
Nebula - Charged
New End Orignal - Thriller
Nine Inch Nails - Year Zero
Oceansize - Everyone into Position
Onelinedrawing - the Volunteers
Peaches - Fatherfucker
Pearl Jam
Peter Bjorn and John - Writer's Block
PJ Harvey - Stories from the City...
Poison the Well - You Came Before You
Polyphonic Spree - The Beginning Stages of
Postal Service - Give Up
Probot
The Prodigy - Invaders Must Die
Queen Adreena - Drink Me
Queens of the Stone Age - Songs for the Deaf
Radiohead - In Rainbows
Rage Against the Machine - Renegades
Regina Spektor - Begin to Hope
Reuben - In Nothing We Trust
Rival Schools - United By Fate
Russian Circles - Geneva
Saul Williams
Seasick Steve - I started out with nothing...
Shad - TSOL
She and Him - Volume Two
Shellac - 1000 Hurts
Sigur Ros - Takk
Sleigh Bells - Treats
Slow Club - Yeah So
Smashing Pumpkins - Machina II
Sparta - Wiretap Scars
Stars - Set Yourself on Fire
Strapping Young Lad
Sufjan Stevens - Illinoise
System of A Down - Toxicity
Tallest Man on Earth - The Wild Hunt
Temper Trap - Conditions
Test Icicles - For Screening Purposes Only
Them Crooked Vultures
These Arms Are Snakes - Tail Swallower and Dove
Thom Yorke - The Eraser
Thursday - Full Collapse
Titus Andronicus - The Monitor
Tool - Lateralus
TV On the Radio - Dear Science
Twilight Singers - She Loves You
Two Door Cinema Club - Tourist History
UNKLE - Never, Never Land
Walter Schreifels - An Open Letter to the Scene
White Stripes - White Blood Cells
William Shatner - Has Been
Yeah Yeah Yeahs - Fever To Tell
Yourcodenames:milo - Ignoto
Yuck
65daysofstatic - We Were Exploding Anyway
//
So there