TCG2 route for guide

Black Box Zapdos: Base Set Raichu (Assault) + Base Set Zapdos (Premier) + Dark Raichu (Ambition) (You will never get this probably, but if you have these cards and use the Black Box in the Game Corner, you'll get the legendary Zapdos early, which you should probably use as much as possible, including in the Pokemon Dome)

Auto Deck Machine Packs (Save pack 1 and 2 if you're scared about Colorless Altar; I like to open them, since pack 1 can have a lot of nice Pokemon, and pack 2 can have PlusPower/Defender):
1 - Pikachu, Rattata, Meowth
2 - DCE, Spearow, Jigglypuff, Dratini
3 - Pikachu, Fossil, Meowth
4 - Pidgey

The beginning duels are very harsh, due to a lot of dual-type decks that prevent easy weakness abuse. These are the edits I ended up doing for them. I used to use Diglett against Lightning Club, but he gets so walled against the Pidgeys and Doduos that it ain't worth it. Note that if you get Dugtrio, you might wanna use him.
For the early game, I tend to try to have 30 Trainers in the deck with two Pokemon families. It can be very tight on energy, go heavier on Fire energy since you'll be discarding it for embers.
The AI always declines Challenge!, so it acts as a second set of Bills late game.
My trainers early would tend to be something like:
MAX Bill, Oak, Energy Search, PlusPower, Energy Removal
1 or 2 Energy Retrieval (esp. with Fire energy)
2-3 Gust
2 Full Heal
A good amount of recovery (maybe 1 Super, 1-2 Defender, 2-3 Potion)
2 Switch, maybe Poke Ball/Pokemon Trader

When reducing families, and especially using Fat Pikachu/Magikarps, max out recovery trainers. Fossil is great for Magikarp survival too. Using 1 Pokemon decks (Scyther/Hungry Snorlax), definitely put as many useful trainers in as possible like Gusts and Energy Removals, energy shouldn't be an issue.

These RECONs mean just use that family (Bulbasaur+Ivysaur, Charmander+Charmeleon, etc), and edit your energy types accordingly.
This is what ends up being in the deck machine with this route (slot 6 and 7 used to minimize keypresses)
Slot 1: Charmander only deck
Slot 2: Electric/Fighting deck
Slot 6: Electric only deck
Slot 7: Water deck (usually Magikarp only; Seel/Dewgong can be good too, however Rapid Evolution and no guaranteed Computer Search makes Magikarp far more reliable, although fragile pre-evolution)

[Grass Club], free booster packs, duel Brittany
[Ishihara's House] to Nikki, get free deck, dismantle Starter Deck
[Rock Club], OPEN MAIL PACK 1, RECON: Bulbasaur/Paras
[Grass/Science Club], DISMANTLE SLOT 1, RECON: Bulbasaur/Charmander
[Water Club], RECON: Charmander ONLY, GR3, then [Fire Club], RECON/SAVE: Dismantle top, improve deck, SAVE TO MACHINE, GR3 again
Lose to Ronald
[Lightning Club], SAVE BEFORE DUELS
[Psychic Club], duel Murray (Blink Kadabra is huge threat)
RECON: OPEN MAIL PACK 2, dismantle first slot deck, add Pikachu, Speedball Voltorb, trainers
Duel GR4
[Fighting Club], RECON/SAVE (SLOT 2): Remove Charmander, go up to 4 Pikachu, add Diglett/Hitmonchan, SAVE, fight GR1 (You could use Bulba/Diglett? Poliwags can be the biggest issue in this fight. won't have lightning/fighting deck saved tho)
Airport

[Grass Fortress]
Lose to Ronald
LOAD/RECON/SAVE: Fire Deck, add Rocket Charmanders/Trainers, overwrite old Fire deck
BEFORE [THIRD DUEL]:
RECON: Grass Energy ONLY, Bulbasaur/Ivysaur, Scyther?
SAVE BEFORE DUEL (poison-heavy deck, watch out for upskirt grimer, he's insanely strong)
AFTER THIRD DUEL, reload Fire deck

[Electric Fortress]
LOAD/RECON/SAVE: Slot 2, be at FOUR PIKACHUS (reduce Voltorb/Electabuzz), overwrite Slot 2
Duel Pikachu girl
RECON/SAVE (SLOT 6): Lightning Energy only, Voltorb, Electabuzz (Raichu filler?) (This edit always needs filler, you have a low amount of Lightning energy. Vending Raichu kinda sucks, but its Thunderbolt can be good for a last turn attack)
SAVE BEFORE DUEL, duel Chip (one of the hardest duels)
LOAD/RECON: Electric/Fighting Deck (slot 2), reduce Pikachu to add Speedball Voltorb
Duel leader (Electric do +10; Speedball Voltorb one-shots Doduos), leave

[Water Fortress] (right/down)
Always save before duels where you use Magikarp, and know when you won't be able to Rapid Evolve in time. They can be very hard duels, especially because these trainers have Energy Removals.
RECON/SAVE: Water Energy, Magikarp/Gyarados (and Dewgong?) (SAVE THIS DECK TO 7) (You NEED 4 Magikarp in it for a deck requirement; if you don't have 4 Rocket Magikarp, be sure to remove the Base Set Magikarps in the Dome)
Save, fight Jacob and Cody
LOAD: Lightning Deck (SLOT 6)
Duel Alex and Brooke, lose to Ronald

[Fire Fortress] (up/up)
Oddly, Water types are never used here. Magikarp is far too flimsy to survive against Flame Tail Charmanders and Magmars, there's a fire energy only duel, Charmander/Charmeleon is generally the most reliable Stage 1 in the game, and the leader's special rule is that Fire types have no weakness.
LOAD: Fire Deck (slot 1)
Duel Jess and Kara
RECON: Add 4 Eevees
Duel Ellen (Save first, reset if Eevee only in hand)
LOAD: Fire Deck (slot 1)
Duel Bernard

[Fighting Fortress] (right/right)
If you don't have a Scyther, this might not go super well.
Right doorway, up, right, down, booster, right, up
RECON: ONLY FIGHTING ENERGY, Scyther only (or Paras/Parasect only)
Down, left, up, up, up, booster, left, up, left, left, down, left, up
RECON: Grass/DCE/Potion/Full Heal Energy, Bulbasaur/Ivysaur (or just Scyther), NO ENERGY REMOVALS
Down, right, down into pit, climb stairs, duel Brutus (The special rule is that Fighting resistances don't exist, so have recovery items handy. A confused Dark Primeape can one-shot you, but you can oneshot it with a swords dance slash, probably max out Gusts)

[Psychic Stronghold] (up)
CREATE NEW DECK: Hungry Snorlax, energies (FULL HEAL/POTION)
Fight no trainers girl (top right)
Dismantle that deck, RECON: Hungry Snorlax, Psychic energy only, readd Energy Removals
Fight left 2 people and the boss
NOTE: You may want to try using the Scyther deck against the boy on the left; he has 2 Rocket Machop and 2 Hitmonchan that, if he gets lucky, can destroy Hungry Snorlax.  At the very least, I suggest fighting the Psychic-only girl first, then editing to add Potion/Full Heal/DCE energy for the boy and the boss, for a little edge.
The boss is probably the worst duel in the game; the only thing that can kill you, however, is being shuffled into the deck by Dark Gengar. She has a ton of Energy Removals, and even Computer Search/Item Finders for them. It's fairly likely you win by her decking out if things go poorly. I suggest resetting over a Kangaskhan lead, as the card draw will make it far more likely you get screwed. Slowpoke lead is easy, and will stay in forever. If you can make it to turn 3 without being removaled, you're good.

[Airport] (left/left/left/etc), then Pokemon Dome
LOAD/RECON/SAVE: Water Deck (slot 7), add Dewgong if you've gotten it, tweak Trainers (Challenge!, Fossils), overwrite Water Deck
Fight Courtney
LOAD: Fire Deck (Slot 1) (or use Dugtrio?)
SAVE, fight Steve
LOAD: Water Deck (Slot 7)
SAVE, fight Jack, SAVE, fight Rod, go to Airport

[Colorless Altar] (right/right/right/etc/down)
BE VERY CAREFUL HERE, as saving with a bad requirement already given means run over. Edit and save before talking to them for the first time. Check for requirements (bottom to top):
4 Double Colorless or [[Spearow]] or Pidgey? (You will probably only have 1 DCE/Pidgey)
4 Jigglypuff or Dratini or Mysterious Fossil? (Fossil preferred, so you're guaranteed Zapdos. Dratini is the most common)
4 [[Dark Pokemon]]. Use only evolutions, so you're guaranteed Zapdos

When you're not guaranteed Zapdos (only 20% chance here), it can be fairly frustrating to have to reset over both the condition, and not having a way to get Zapdos out...

If you're short just one Jigglypuff/Dratini (which you may be), you can use pack 2. Or short one Fossil, use pack 3 (delete 4 emails and exit/re-enter Colorless Altar to receive it)

Auto Deck Machine Packs:
1 - Pikachu, Rattata, Meowth
2 - DCE, Spearow, Jigglypuff, Dratini
3 - Fossil, Meowth
4 - Pidgey

If you're missing one requirement, try fighting the other guys first. In particular, the top guy gives 2 Lost Isles, which can help reach a Fossil requirement along with mail pack 3. Try to end with the top guy if you can, since only he gives you the coin.

RECON FOR BOTTOM GUY: Machop/Machoke! Energy will be tight here, but Machoke works far better than Zapdos against his army of 90-120 HP basics.

RECON FOR TOP TWO: Zapdos deck + Whatever they want (REMOVE POKEBALL, TRADER, FOSSIL, SWITCH, MAX OUT LIGHTNING ENERGY)

After all three, to lose to Ronald, remove Zapdos and replace it with an easy Basic (base set Pidgey is good if you have one; it's at the top of colorless, and has Whirlwind), DO NOT USE A PSYCHIC-RESIST POKE

[GR Castle] (left/right), lose to Ronald
RECON FOR FIRST DUEL: Add the Legendary Cards, and SAVE
After duel, say no and remove Moltres/Articuno, REMOVE POKEMON TRADER, ADD GOOP GAS ATTACK!! (The girl can have Mr. Mime, which walls Zapdos)
Finish, it should be free from here since you have only Zapdos