I consider cards fall in few categories or ranks; "Staples", "Near Staples", "Techy/Niches" and "Draw". I'll use these to sort of group the card priorities in deck building.
Staple cards are those such as Professor Juniper and VS Seeker. If there is a card you want to be constantly drawing throughout every game, I'd consider it a staple, and most important in deck building. Stadiums and cards that actually make your strategy work generally fall into this category.
I then have cards that I consider "Near Staples". You can probably play a deck fine without it, but the card fills a common niche hence its utility. This includes things like Lysandre and Hoopa-EX, as both can positively effect each game. I generally run one or two of these, as I don't necessarily
need them.
I then have the more Techy/Niche cards. These are generally the cards that can be really useful against certain matchups. This would include things like Enhanced Hammer and Head Ringer, which are really defined in what they affect. They are also dead cards in certain matchups (such as decks using no Special Energy or no EXs), which is why they are last priority. These often only have a couple of copies each as well, for the said reason.
Additional draw and consistency cards are probably least in priority. This includes things like Acro Bike and Trainer's Mail, which simply quicken up your deck. This does not include things like Ultra Ball and Shaymin-EX, as they are more so staples. That said, extra of these said staples may fall into this category. By the time I finish deck building, I rarely have space for extra draw, although simple, solid decks such as Manectric-EX utilise draw power quite well.
Hope that helps. :3