It's not that complicated, seriously.
1. For a normal deck, just run an extra consistency card. And don't deck out, doofus.
2, For a normal deck that is especially prone to running out of resources of a certain type, like how old Fairy decks ran out of energy or Garchomp Altaria can be messed up by losing one of the evolution chain early, add the specific card that gets the resource back, like energy retrieval or sacred ash. And don't deck out, doofus.
3. For a speed deck, either tone down the speed draw cards a little, or keep them in and play more cautiously. And don't deck out, doofus.
Not decking out is so simple. Just be a little thoughtful. Don't dump hands full of resources just in the hope of getting a slightly better card you don't really need. Don't burn two cards to ultraball for a Pokemon you don't really need. Be willing not to dump amd draw sometimes because what you would give up, compared to what you would gain, is not worth it.