Okay, leaving right before HGSS means you've missed Primes and Legends (HGSS, Unleashed, Undaunted, Triumohant).
Primes are basically a super-rare card with a fancy border that tends to be better than a regular card of that name (eg Magnezone Prime; the card text only says "Magnezone" so it can be played as a regular Magnezone card. It evolves from Magneton still and can Level-Up to Magnezone Lv.X, it's just considered to be pretty good).
Also, Legends are two cards you put together by the long side to make one piece of artwork, which functions as 1 pokémon (eg Ho-Oh Legend, although most Legend cards picture 2 Pokémon, eg Rayquaza & Deoxys Legend). The ones that picture one pokémon give 1 prize card if KO'd, the ones that picture 2 give 2 prize cards (that's what it's been up til now, at least, but it may change). These have special rules, which you can find on bulbapedia for more detail...
The archetypes that are from HGSS are... VileGar, Donphan Prime (Donkphan), Steelix Prime, and I think that's it (unless you want to count Scizor Prime). SP decks are still very powerful (Luxchomp and DialgaChomp, a lot) as well as Gyarados. Nothing really comes to mind in particular right now, but I'm sure others will correct me where I've missed info.
Welcome back!