What is the best Pokemon in HeartGold and SoulSilver?

Gyarados gets a massive boost from the physical/special split. In the original GS, its 125 Attack was wasted on special Water moves. Now it gets physical Waterfall. The Red Gyarados at Lake of Rage is still free, still Level 30, and now one of the best Pokemon in the game instead of just a cool shiny. Dragonite at 600 BST is the pseudo-legendary, but Dratini comes late.

What is the best starter in HeartGold and SoulSilver?

Cyndaquil is still the most efficient. Typhlosion's 109 Sp. Atk and 100 Speed carry through both regions. Totodile gets a massive upgrade though — Feraligatr's 105 Attack now works with physical Waterfall and Ice Punch. The gap between starters is much smaller in HGSS than in the originals.

How does the physical/special split change the HGSS tier list?

In the original Gold and Silver, moves were physical or special based on TYPE. All Water moves were special, all Ghost moves were physical. That crippled Pokemon like Feraligatr (105 Atk but forced into special Water moves) and Gengar (130 Sp. Atk but stuck with physical Ghost). HGSS runs on Gen 4's engine where each move has its own category. Feraligatr and Gyarados jump multiple tiers because of this.

Which version exclusives are better, HeartGold or SoulSilver?

HeartGold gets Ho-Oh at Level 45 before the Elite Four and exclusives like Growlithe, Mankey, and Gligar. SoulSilver gets Lugia at Level 45 and Vulpix, Meowth, and Teddiursa. Ho-Oh hits harder offensively while Lugia is one of the best defensive walls ever. Both are strong for the main playthrough.

What's the best team for an HGSS playthrough?

Typhlosion (starter), Red Gyarados from Lake of Rage, Espeon from Bill's Eevee, Heracross from headbutt trees, Ampharos from Mareep on Route 32, and Dragonite from Dratini in the Dragon's Den. Swap Dragonite for Machamp if you don't want to grind Dratini to Level 55.

Is the Red Gyarados better in HGSS than in the original Gold and Silver?

Much better. In GS, Gyarados was stuck using special Water moves with its terrible 60 Sp. Atk. Its 125 Attack was mostly wasted. In HGSS, Waterfall is physical, so Gyarados finally hits as hard as its stats suggest. Add Intimidate (didn't exist in Gen 2) and Ice Fang for coverage, and it goes from a solid team member to one of the best Pokemon in the game.

Is Dragonite worth the grind in HGSS?

Dragonite has 600 BST and Dragon/Flying typing with great coverage options. The grind: Dratini doesn't become Dragonair until Level 30, and Dragonair doesn't become Dragonite until Level 55. If you catch Dratini early from the Dragon's Den or Game Corner, you'll spend serious time leveling. Worth it for Kanto and the post-game, but you can beat the Johto Elite Four without it.

Pokemon HeartGold & SoulSilver Tier List

HGSS remakes Gold and Silver on Gen 4's engine, and the physical/special split changes the tier list completely. Feraligatr was held back in the originals because Water was a special type, but now it uses its 105 Attack properly with Waterfall and Ice Punch. Gyarados gets the same upgrade with 125 Attack on physical Water moves. Typhlosion is still the fastest starter, but the gap is narrower now. Same two-region adventure, completely different power dynamics.