At the turn of Gen 5, Nintendo was still dominating the market with just how many exclusivity deals they had with third party developers. The decision to continue losing cartridges was what caused those companies to jump ship, simply because disc based media had a much higher storage capacity that meant their games could not even fit on cartridges anymore.
If the Nintendo 64 used CDs, those developers would have stayed with Nintendo. You could argue that those developers would have gone multiplatform, but at the time Nintendo was untouchable, so you have to wonder if the developers would even consider doing that. So it is a tough question to answer, but I think just due to their domination of the market at the time, Nintendo would have won