What are the differences within/between Pokemon series?
It's not the set theirselves, it's the "era". BW: Dragons Exalted and BW: Emerging Powers are from the same era and share the same mechanics (although starting from BW: Next Destinies Pokémon EX were introduced, and from BW: Plasma Storm we got Team Plasma cards with certain advantages when combined with other cards that give them effects).

However, the Black &amp; White series and the HeartGold &amp; SoulSilver series are different in that, given the former has Pokémon EX and Team Plasma Pokémon, the latter has Pokémon Prime and Pokémon LEGEND (Prime cards are more powerful versions of certain Pokémon, and LEGEND cards are Pokémon that can only be played by having both parts of the whole card in your hand).

Sometimes the rules change over the eras aswell. In BW some cards received errata (such as Rare Candy) and certain rules were reworked (such as who goes first), but besides that the game remains largely the same.

Hope that helps.