That's a massive exaggeration.
" Aside from wanting us to change the atmosphere a lot, there were two main things that Miyamoto-san said from the start of the project—"It's fine without a story, so do we really need one?" and "As much as possible, complete it with only characters from the Super Mario world. "
Neither are a case of him outright demanding it to be different in the way you're saying.
iwataasks.nintendo.com
In addition, the story thing was completely on Intelligent Systems(and more specifically one person), a different subset of people from regular Nintendo(yes, there's multiple divisions), who basically screwed up with their poll, asking the wrong question. For that matter, the card thing was already planned separately from anything Miyamoto said. Because they felt it was better to spice up the game with what their boss said kept in mind, the card system went from being a partial gimmick to the main way to play. (Hell, even the TVTropes page is misleading about his "demands". That's not the case here). Now, he did say it was "boring" in context of essentially being a part of the GC game. Understandably, that's a pretty major thing to hear, and since they want his approval, changed it in a heartbeat.
To further emphasize the issue with the story factor; while it's not nearly as massive as people think it is as an issue, they basically put a poll out on Club Nintendo with a poor wording. What happened is a very tiny pool of people had no clue they meant "rpg stories", thus, leading to a skewed set of answers. However, keeping in mind it's the best selling Paper Mario game to date in Japan, this also means that it caters to that audience better, which is pretty important to why the same direction was kept.
So basically; you can't blame all of Nintendo when it's a very select few people(which also makes this thread kind of weird, since it's never going to be all of Nintendo that makes an error) who caused the issue with the series for part of the fanbase, and then expect us to listen when you spread falsehoods of what actually happened. It's at most 3 people that affected this, and it's not even all of Intelligent Systems anyway. I don't like the new direction either(though some concepts of it, yes). But I also, as a game designer myself, knows it's not that simple. Frankly, I have things I'd love to blame on them too... but I know that's just pointless vitriol that rarely makes sense.