Gold, Silver, and Crystal take place in the Johto region, with a brief jaunt through Kanto after defeating the Elite Four. Commonly considered the best of the series, these games introduced many features that are now taken for granted, such as hold items and genders.
Starter Pokémon
You can start with 3 Pokémon in these games. Chikorita, Totodile, and Cyndaquil.
If you start with Chikorita, your rival steals Cyndaquil. Useful counters include: Chinchou, Corsola, Geodude, Goldeen, Horsea, Krabby, Lapras, Marill, Onix, Psyduck, Remoraid, Sandshrew, Slowpoke, Staryu, Sudowoodo, Swinub, Tentacool, and Wooper.
If you start with Cyndaquil, your rival steals Totodile. Useful Johto counters include Bellsprout, Hoppip, Chinchou, Oddish, Mareep, Sunkern, and Voltorb.
If you start with Totodile, your rival steals Chikorita. Some useful Pokémon for type coverages include Pidgey, Spearow, Growlithe (Gold only), and Vulpix (Silver only).
What Starter Should I use?
As with all Pokémon games, one's choice in starter Pokémon is largely irrelevant.
Totodile's line focuses on Attack. Feraligatr may end up being useless as a water type, as its stats are built for being a physical sweeper, while Water is a special type. However, it can still kick ass and take names with Earthquake among other things.
Cyndaquil's line focuses on Special Attack, although it generally is more balanced. Typhlosion is quite useful, what with the various elemental punches, and continues to be a fine choice for a fire type throughout the game.
Chikorita is best if you like playing in what is effectively hard mode. Almost all Johto gym leaders use types that will make mincemeat out of Chikorita, and by the time you've reached Kanto, you have plenty of other options for an easily-ignored type if you absolutely must have a grass type. Meganium isn't even particularly useful competitively.
Just pick the starter Pokémon you like best. It won't make much of a difference in the long run.
Catching the Legendary Beasts
First of all, the Masterball is your friend, forever and always. Second, Mean Look and Spider Web are nigh useless, as they all know Roar. All you really need is a fast Pokémon with False Swipe and a bit of patience.
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