Ezren earning a card feat when only divine spells are available is a specific setting, and not a bad one. So Ezren got a cure scroll? Sounds damn fun to me. Adventuring lead to unexpected and weird rewards. And a better spell is likely to popup in the following scenario.
Somebody don't like it? He prefers to stick to no-brainers? Good for him, I'm not judging. I'll just notice that it won't happen much (new card feat + lame choice of cards).
I'm not in the designer team, but my guess is that the rule making you choose a card in a box (if nothing else is available) is only there to prevent incomplete decks. Whe should consider ourself luck that it's not a random draw.
So basically you're saying that the cards you want to get rid of your deck are not bad, but that better ones exists in the box. If it is, I'm sorry, but you've picked the wrong game. Building a deck with cards you gather during the adventure is part of the intended gameplay, and nowhere in the game design it is ruled that you'll get access to the cards you want no matter what. Pathfinder ACG is a game about finding stuff, not building the perfect deck from a thousand cards. Games like Magic the Gathering fill that niche, and they're good for that.
But as other have stated before, it is your game, feel free to customize it if you enjoy it more that way. If I were you, I'll just swap the cards of my deck with cards from the box between adventures. Just consider it a house rule. The way you write it in your first post, it feels like you want to twist the rules to use them against themselves.
At the risk of being a total downer... does it concern anyone that this releasing may be the death of the physical card game? It's shaping up to look like this is the superior version of the game in every way and if it delivers, I can see Mask of the Mummy being the physical game's last AP. Part of me is disturbed by the idea but the other half would be happy to convert. As I write this I'm sitting in a room lined with games from the modern consoles running back to the Atari, so I definitely can't say I wouldn't get behind a video game version.
I really don't see that happening. The digital release may be more convenient for solo play, but that's about it, even with new features. Board games lovers like the physical feel of their games, even if that means sorting their cards themselves. Websites like boardgamearena offer free online multiplayer board games for years, with little if no consequence in term of market.