I think the most important thing to decide first is what kind of deck you want to play. Look around the Deck Garage forum, and playtest decks that sound fun or interesting in online simulators (such as PlayTCG (free, but manual), PTCGO (generally costly, but an automatic interface), or TCGOne (Automatic, but lacks some modified format cards) until you choose one or a handful of decks that you really like.
Once you've found some, you can compare those decks based on their price (which you can do either by checking prices on eBay's sold listings or through an online store for singles such as Troll and Toad or Collectors cache) and their reliance of cards that will likely be rotated out at the end of the season (which occurs each September, this time rotating to Boundaries Crossed-On).
Then you must decide based on all three factors: fun (most important), price, and lifetime (i.e. how many seasons from now this deck might be able to last).
As for specific suggestions, you might choose a less common deck like Flareon, and thus sacrifice lifetime for a lower price (still keeping in mind the enjoy-ability of the deck above all else). Or you might choose a more adaptable deck like Aromatisse + Techs (the other way around from Flareon, as you can essentially just keep on adding in and taking out attackers until Aromatisse itself rotates out in 2-3 years).
Keep in mind that even if you choose a deck that gets mostly rotated out, not all of your cards are immediately worthless. Many staple cards get reprinted numerous times, lasting for years, and are also usable in pretty much any deck, meaning you rarely have to spend the money on them twice. Also, with the Extended (Black and White-On) Format being started next season, those cards will always be playable somewhere, and thus will maintain at least some of their value.
