I have made visual guides that show the path that can be taken in order to clear through each region collecting only necessary items.
Kanto: https://www.youtube.com/watch?v=4Cp6QSxHYbY&t=13s
Unova: https://www.youtube.com/watch?v=Z6IMUk90e-0&t=8s
Hoenn: https://www.youtube.com/watch?v=47BLpTPZm9s&t=5s
Sinnoh: https://www.youtube.com/watch?v=u3LYBlSEy30&t=33s
Johto: https://www.youtube.com/watch?v=hWf__XFW1kM&t=532s
If you are interested in a guide for items you can follow this guide here: https://forums.pokemmo.com/index.php?/topic/76529-storyline-guide-kanto-johto-hoenn-sinnoh-unova-complete-walkthrough-all-items-hidden-items/
Which I have also made visual guides for which can be found here.
Kanto: https://www.youtube.com/watch?v=1rWB0kDHSdc&t=7s
Unova: https://www.youtube.com/watch?v=BUUyZWRM8-A&t=1736s
Hoenn: https://www.youtube.com/watch?v=q0I4CbaVY-o&t=1097s
Sinnoh: https://www.youtube.com/watch?v=mc4W52ir2KY&t=1171s
Johto: https://www.youtube.com/watch?v=9ZB2nB4rDUw
These were the Pokemon that I used.
Cloyster
Nature: Adamant
IVs: 25+ Attack 25+ Speed
EVs: 252 Attack 252 Speed 6 HP
Ability: Skill Link
Moveset: Ice shard, Icicle Spear, Rock Blast, Shell Smash
Items: NeverMeltIce, Wide Lens, Focus Sash
Krookodile
Nature: Adamant
IVs: 25+ Attack 25+ Speed
EVs: 252 Attack 252 Speed 6 HP
Ability: Moxie
Moveset: Earthquake, Crunch, Dig, Assurance
Items: Soft Sand, Black Glasses
Starmie
Nature: Modest
IVs: 25+ Special Attack 25+ Speed
EVs: 252 Special Attack 252 Speed 6 HP
Ability: N/A (Natural Cure Ideal)
Moveset: Surf, Psychic, Thunderbolt, Power Gem
Items: Mystic Water, Twisted Spoon, Magnet
Dragonite
Nature: N/A
IVs: N/A
EVs: N/A
Ability: N/A
Moveset: Waterfall, Fly, Defog, Whirlpool
Items: N/A
Bibarel
Nature: N/A
IVs: N/A
EVs: N/A
Ability: N/A
Moveset: Dive, Strength, Rock Smash, Rock Climb
Items: N/A
Starter
Nature: N/A
IVs: N/A
EVs: N/A
Ability: N/A
Moveset: Cut, Flash, N/A, N/A
Items: N/A
This combination allowed me to have all HMs at all times teaching cut and flash when needed to my starter. Starmie was used only in some regions, I would recommend it for Johto as it has some of the tougher fights if you are under leveled.