Much like Doom 3, Nuts & Bolts isn't bad, just completely different than what the fanbase of 3D Collectathon platformers wanted after Microsoft purchased Rare. Even in 2008, the genre had already sort of wilted away. Fans of the genre and of the series were itching for a new game after 8 years to collect those 100 jiggies in, but the new direction turned a lot of those fans away.
Now, again, Nuts & Bolts is a good game. In fact, I would say it was ahead of its time, coming out just before sandbox games like Minecraft became huge sensations and had these massive reverberations across game design we still feel today. Hell, there were a lot of people calling Tears of the Kingdom "The Legend of Zelda: Nuts & Bolts" without a hint of derision against TotK.
And that's just it: Nuts & Bolts came out at the wrong time.
In 2008, fan mistrust of Microsoft doing right by the beloved Rare franchises was very low after Perfect Dark Zero and the Xbox remake of Conker (even with Viva Pinata being a delight). What Microsoft needed to do to get that trust back was to hit a very safe, conservative, fan pleasing game out of Rare. If they did that, built up that trust, and made Nuts & Bolts afterwards, new IP or not, I think it would have a very different legacy today.
Instead they took a risk on bringing a beloved franchise into a completely new direction and, even with good word of mouth from those who played it and enjoyed it, it was a commercial failure. Not only that, but the trust in Microsoft tanked from Rare fans and 3D platformer fans mourned the death of yet another franchise.
And... Rare never really came back from Nuts & Bolts. They got put on Kinect titles for the next few years and had a hand in Killer Instinct's revival (though most of that was Double Helix and Iron Galaxy), but by the time Sea of Thieves came along, Rare was a completely different company. Their legacy was gone and, honestly, so were most of their fans.