It was a flop in terms of... they messed up the CD deal with Sony and as a result invited Sony into the console market. They pretty much made themselves a massive rival that beat the shit out of their offerings, the only way to look at Sony joining the console market as a + for Nintendo is that Sony did make it "cool" for teens and above to be gamers with the playstation generation and some of the dark games like Resi Evil which were not aimed at kids.
It was a flop in terms of what it did for 3rd party support, absolutely burning bridges with the likes of Squaresoft was idiotic on the part of Nintendo and the N64 was a middle finger to developers with it's expensive and out dated cartridge.
It was a flop considering that the CPU of it was being compared to supercomputers at the time it was being developed... then they put 4mb of ram in it and an absolutely miniscule texture cache, they made a bottleneck machine basically.
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When i say 'mediocre' i'm talking purely in reference to its sales in the context of the competition it was up against. As a whole i'd personally consider it a failure. They shouldn't have had to lose $5b to achieve those sales.