Man, I'm kind of conflicted on this idea. Replacing the mini-games with standard fetch quests or kill X monster quests would kill some of the charm that this game has. In all likelihood I've played hundreds of jrpg style games since first playing Dragon Warrior on the NES. And of those hundreds of games probably 90% stuck to the base fetch and kill quests - and those games have all faded into a bland haze in my memory. But the ones that have done something different, who threw in some interesting side mechanics do stand out in my memory - but not always for good reasons. Sometimes the goofy side mechanics make the game annoying. So I think the Dev team is going to have to walk a fine line here.
The only puzzle they used in the v13 release that bothered me was the jumping puzzle, which was pretty difficult and forced me to save scum. But I did beat it in less than 20 minutes. That wasn't too bad, and would even be pretty appropriate for a near end of game puzzle. When they went to the new puzzles, I found them to be much easier but still interesting. Like I said I only had to restart the Challenge of Strength once to beat it. I don't think the issue is the difficulty of these puzzles, but more of the fact that some players don't want to have to deal with them in their pursuit of a story/fap.
I can see the allure of allowing the players to choose to skip a puzzle, but it is going to make the game much more boring if the players do so. But I guess if they are only playing it for a quick/easy fap then they aren't interested in the gameplay much anyway. But replacing the puzzles with standard fetch and kill quests would likely do the same, with no option for the player to experience any different gameplay.