I don't particularly care one way or another, and I apologize if this has been answered before, but can you give an example where an action would not work with the previous shuffling rule?
In games with published cards, the only issues are confusing people when the things you do with the cards are more involved (e.g. Lookout), and people forgetting how many cards they've drawn for that Smithy. Those are both significant issues so I am glad to have addressed them.
It is easy to make an unpublished card that creates issues, and you can argue in each case "oh but instead that could say, set aside the top 3 cards, then do this thing." You still have confusion because it isn't clear to everyone that you shuffle to finish doing the setting aside before continuing. It's not great otherwise.
You can also say, "okay that unpublished card doesn't do what you intended sometimes, but you can still resolve it, therefore no problem." If you say that, I disagree.
The game did not start out having much "When x happens, do y." It has a bunch of it now. If you have some more complex command for multiple cards, something may trigger off of it; thus all sorts of things can happen in the middle. For example there was an attack that could trash the top 2 cards of everyone else's deck (somehow it did not survive). But things trigger on trashing; they'd happen for the first card before you shuffled.