I think the main problems people have with the system is that it's an invasive game play element. People want to play the game in their defined role, or as a solo hermit, and the system is invasive to both of these play styles by giving the arbitrary and mandatory objectives that don't allign with their surroundings or play style. In the late game, the quests you must do get absolutely ridiculous in number, and the randomness in difficulty lead to an unfair game play experience. There's nothing worse than getting a quest that basically says "Quest: Press the Abandon button Reward: Lose 1 quest progression," especially when you have to grind out 30+ at a time.
The reason I think it's intrusive is because you could mine your entire hearthling's life, but never be a miner, because the quests are too clunky and don't flow well with normal game play, so my idea is a way to fix that.
Make it so to complete a credo, you fill a progression bar as you do what your credo entails. Got the farming credo? Plant and harvest crops. Pearldiver? Collect mussels and go for long swims. Make it so normal game play affects your progression within the credo and make it so that it takes longer to fill this progression bar the more credos you have previously completed. This isn't to say to do away with the quests either, the quest objectives should stay, but instead provide bonuses to fill the progression bar faster. There are a lot of ways this could be implemented and twisted, but as long as normal game play affects credo progression, I think that'll clean up the system as a whole.
Tl;dr: Allow the normal hearthling grind to help us progress our credos, while making the quests sub objectives instead of mandatory ones.