The rules for deck-building say that you need at least 50 cards, but the rules for the first game setup only mention using 36 cards?? I haven't played the game yet, but it seems like the first game is the same rules as the regular game, so why the reduced deck size?

The first game suggestion to use only the pre-constructed decks (plus neutrals) is there to help you learn the rules, mechanics and flow of the game before adding in the additional variables of deck building. After all, what you learn from the experience of playing a game, even one with fewer cards in the deck, is likely to be a big help in guiding your deck building. It's just a suggestion to walk before you run.

Really, if you have just one copy of the Core Set, the first game suggestion is simply to play a game with a single faction before trying to figure out who you should ally with.

The initial core setup is there to get you up and running quickly: simply grab the faction you want and chuck in half the neutrals and away you go.

Mechanically there is no difference between the rules used for these decks and customised ones (they just use fewer cards). But it does mean that you will see slightly more occurrence of the signature cards than you would when using a "full" deck. It might also be possible to get into a situation were it is easier to run out of cards, but I've not managed to have this happen as yet.

It's a good way to learn the game, but don't be surprised to see some (large) holes in some of the faction decks, some matchups will be easier than others and that is where the deckbuilding comes in.

Thanks for the responses. Hope to play it soon!