Here is the new numbering system seen in Ruby/Sapphire. These are for the Pokémon which are unobtainable in R/S:
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#203 Bulbasaur - #204 Ivysaur - #205 Venusaur
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#206 Charmander - #205 Charmeleon - #206 Charizard
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#209 Squirtle - #210 Wartortle - #211 Blastoise
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#212 Caterpie - #213 Metapod - #214 Butterfree
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#215 Weedle - #216 Kakuna - #217 Beedrill
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#218 Pidgey - #219 Pidgeotto - #220 Pidgeot
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#221 Rattata - #222 Raticate
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#223 Spearow - #224 Fearow
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#225 Ekans - #226 Arbok
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#227 Nidoran - #228 Nidorina - #229 Nidoqueen
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#230 Nidoran - #231 Nidorino - #232 Nidoking
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#233 Clefairy - #234 Clefable
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#235 Paras - #236 Parasect
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#237 Venonat - #238 Venomoth
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#239 Diglett - #240 Dugtrio
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#241 Meowth - #242 Persian
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#243 Mankey - #244 Primeape
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#245 Growlithe - #246 Arcanine
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#247 Poliwag - #248 Poliwhirl - #250 Poliwrath
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#250 Bellsprout - #251 Weepinbell - #252 Victreebel
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#253 Ponyta - #254 Rapidash
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#255 Slowpoke - #256 Slowbro

#257 Farfetch'd
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#258 Seel - #259 Dewgong
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#260 Shellder - #261 Cloyster
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#262 Gastly - #263 Haunter - #264 Gengar

#265 Onix
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#266 Drowzee - #267 Hypno
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#268 Krabby - #269 Kingler
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#270 Exeggcute - #271 Exeggutor
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#272 Cubone - #273 Marowak
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#274 Hitmonlee / #275 Hitmonchan

#276 Lickitung

#277 Chansey

#278 Tangela

#279 Kangaskahn

#280 Mr. Mime

#281 Scyther

#282 Jynx

#283 Electabuzz

#284 Magmar

#285 Tauros

#286 Lapras

#287 Ditto
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#288 Eevee - #289 Vaporeon / #290 Jolteon / #291 Flareon

#292 Porygon
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#293 Omanyte - #294 Omastar
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#295 Kabuto - #296 Kabutops

#297 Aerodactyl

#298 Snorlax

#299 Articuno

#300 Zapdos

#301 Moltres
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#302 Dratini - #303 Dragonair - #304 Dragonite

#305 Mewtwo

#306 Mew
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#307 Chikorita - #308 Bayleef - #309 Meganium
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#310 Cyndaquil - #311 Quilava - #312 Typhlosion
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#313 Totodile - #314 Croconaw - #315 Feraligatr
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#316 Sentret - #317 Furret
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#318 Hoothoot - #319 Noctowl
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#320 Ledyba - #321 Ledian
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#322 Spinarak - #323 Ariados

#324 Cleffa
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#325 Togepi - #326 Togetic
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#327 Mareep - #328 Flaaffy - #329 Ampharos

#330 Sudowoodo

#331 Politoed
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#332 Hoppip - #333 Skiploom - #334 Jumpluff

#335 Aipom
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#336 Sunkern - #337 Sunflora

#338 Yanma
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#339 Wooper - #340 Quagsire
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#341 Espeon / #342 Umbreon

#343 Murkrow

#344 Slowking

#345 Misdreavus

#346 Unown
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#347 Pineco - #348 Forretress

#349 Dunsparce

#350 Gligar

#351 Steelix
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#352 Snubbull - #353 Granbull

#354 Qwilfish

#355 Scizor

#356 Shuckle

#357 Sneasel
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#358 Teddiursa - #359 Ursaring
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#360 Swinub - #361 Piloswine
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#362 Remoraid - #363 Octillery

#364 Delibird

#365 Mantine
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#366 Houndour - #367 Houndoom

#368 Porygon2

#369 Stantler

#370 Smeargle
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#371 Tyrogue - #372 Hitmontop

#373 Smoochum

#374 Elekid

#375 Magby

#376 Miltank

#377 Blissey

#378 Raikou

#379 Entei

#380 Suicune
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#381 Larvitar - #382 Pupitar - #383 Tyranitar

#384 Lugia

#385 Ho-oh

#386 Celebi
Pokémon Obtainable in Game