The no CD is obviously the biggest one, but another is not letting Rockstar go. Can you imagine if GTA was a Nintendo exclusive?

CDs aren't the only reason the N64 lost to the PS1... the N64 was also alot harder to program for due to bottlenecks in the architecture despite being more powerful than the PS1, which also hurt it's 3rd party support.  Simply swapping out cartridges for a CD-ROM drive wouldn't have solved that problem; the system would've had to have been redesigned from the ground up in order to really take advantage of CDs and be popular with 3rd parties.

And let's not discount the fact that Nintendo had already ruffled plenty of feathers with 3rd party developers in the decade before the N64 launched, so there's still no guarantee all those successful games on PS1 like FFVII and MGS would've definitely been exclusive to the N64 instead of the PS1.

It's actually somewhat hillarious that going into the N64/PS/Saturn era, Nintendo effectively had DMA Design/Rockstar (future makers of Grand Theft Auto), Squaresoft (Final Fantasy, Super Mario RPG), and Enix (Dragon Quest) basically as 2nd party developers. 

Talk about squandering an incredibly favorable position. Final Fantasy, Dragon Quest, and GTA could indeed all have been Nintendo exclusive (two of the three already were basically at that point). 

Cartridge decision had nothing to do with piracy. 

CD-ROM piracy was pretty much unheard of in the early/mid-90s that was never the issue. I remember seeing a CD burner for the first time in like 1996, they were still rare until the later part of the 90s. 

There were various factors, I believe Nintendo had made in the early 90s a large investment in a cartridge factory, and they were reluctant to lose money on that investement. Beyond that developers like Miyamoto didn't like CD-ROM because of loading times. 

Mostly it was likely just arrogance and a lack of vision at the heart of it. Also Miyamoto should've known his place, he's a developer, it should not be his place to dictate company policy and direction. Nintendo could have easily released a N64 with both CD and cartridges, a cartridge slot costs next to nothing if Mario 64 wasn't possible on CD. Never should've been an either/or decision. 

The CD debacle was because of Nintendo having a deal with Sony, but not reading the fine print and realizing too late that Sony would get the software platform royalties. They had to back out at the 11th hour and it was too late to get something properly worked out with Panasonic.

This was Nintendo's "dream team" -strategy; having only selected developers that Nintendo would publish their games. 2nd party was essentially how Nintendo it with NES. The reason for the dream team was because Nintendo believed 3D game development would be so expensive, that most of the industry would go bankrupt. This would ensure the best developers would survive. Of course, the strategy would fail - not because of cartridges or costs associated, but because of the obvious lack of developers, i.e games, on the system. The time Nintendo woke up to the situation, it was already too late. Gamecube, on the other hand, was designed developers in mind (ended up being even worse).

Actually, they did have a lot to do with piracy - though it certainly wasn't the only reason - I don't think it was home piracy Nintendo was worried about, but the mass producers, it really wasn't a stretch to find a store selling pirated NES games circa 1990.

In 1995 CD-burners were already widely available, but the reason you did not see a lot of piracy was because of the cost of a CD-R disc. 1996 or 1997 prices of the discs had already dropped to a level where it made sense to actually pirate a game. Keep in mind that at this time you actually had to have the physical copy of the game in order to have the image.

By 1998 or 1999 it already made sense to pirate only the blockbuster games, because everything else would be sold at the price of a CD-R shortly after launch - leading to a situation where only "dreamteam" would make money off their games.

N64 had the disc drive (in Japan), that would cost only a fraction compared to cartridges  to release games to, but it never took off with 3rd parties.

You don't see the contradiction? Why didn't Sega beat Sony if CD's had something to do with who wins. I mean, Sega had the brand, unlike Sony, Sega had a number of of awesome games, unlike Sony, both had CD's. People focus too much on the manufacturing process, what was Sony's strength, was distribution channel. Nintendo haven't been that big in Japan ever, it's main market have always been North-America, while stumbling in Europe. Europe was where Sony gained the foothold, because everywhere they sold Sony's TV's or even Walkmans, Sony could push Playstations - moreso when the eastern bloc opened to western market, the synergic benefits were just huge. 

The decision to use cartridges for the N64 was made in 1993 or early 1994. This was like 4-5 years before CD-ROM piracy actively became a thing and CD-burners weren't available at that time. 

I doubt it had a significant impact on Nintendo's decisions at that time. In 1993, having a computer with just a regular CD-ROM drive was considered all fancy schmancy, lol.

I remember following the N64's development like crazy, in those days I would go to the book store the first day they got a new issue of EGM or GameFan looking for new N64 info. I still remember reading the N64 wouldn't support CD-ROM in that book store all those years ago in early 1994 and this big sinking feeling in the pit of my stomach like "uh oh ... this feels like a massive mistake". I followed every bit of the N64's development. 

Sure enough I don't think Nintendo has ever really recovered from that mistake in the console business. That decision is where everything went wrong for Nintendo, if they had chosen to compromise instead and included CD for third parties and let Miyamoto and his EAD team use cartridges, hell they could have done CD + cartridge combo games too to save on expensive cartridge sizes (game data could be on the cart, orchestral music and FMVs could've been on the CD disc). 

Saturn was hilariously mismanaged and the 32X pretty much killed the Saturn before it launched.

Even the launch was a disaster, I remember being in Blockbuster Video and turning around and the Saturn was just sitting there on the store shelf, I had no idea Sega had even launched it, lol. There was no TV marketing, and this was the 90s when Sega marketing was everywhere.

Imagine walking into a store tomorrow and just seeing an NX sitting on the store shelf all of the sudden. 

The Saturn was also $399.99 at launch in the US ... which inflation adjusted is $632 today, lol.