It's no different from real baseball cards, with inserts, special inserts, gold and diamond inserts, game used cards, autographed cards, limited edition cards, redeemable cards, series 1, series 2, series 3, traded series etc.
No one's ever realistically going to be able to collect every single card in every single category in most modern baseball card sets (and certainly not all the cards made by a specific company in a specific year) and they probably won't be able to do so in PT either.
They can choose to focus on the categories that interest them though, whether that's base cards, all cards of a certain player, all of a specific team or specific insert series, whatever.
Or they can just build the best team possible, which is what most of the users will want to do.
It's you game, play it your way. It's your collection, build it your way
