Even if you take cutscenes out of it, there's simply almost 90% less space for a game - and cartridges were more expensive for the publisher to boot.
There's no denying that there's great N64 games, but Nintendo crippled the console outside of first and second (Rare) party development. The same trend continued with the Gamecube (despite it being more powerful than the PS2, the Gamecube disc held 25% of the capacity of a PS2 DVD).
If their portables hadn't dominated the market, the mid 90s to mid 00s would've been a terrible time for the company.
Of course Nintendo is doing great now, so you could say it's all a moot point.
