3DS: Launch. The price point and lack of compelling games at launch killed any chance the system had of reaching the same heights as its predecessor the DS. Sure Nintendo was able to save the system with a price drop and great games within the launch year, but it could have sold tens of millions more if it had the right price point and games in Spring 2011 and had the momentum right out of the gate.
Saturn: The shadow launch. Between the price and the pissing off of retailers, it killed the system outside of Japan, and the Saturn was dead on arrival.
Genesis: The focus on add-ons like the Sega CD and the 32X. Their cost, relative lack of games, and sheer bulk were simply unappealing compared to the elegance of the SuperFX chip enhancing SNES games without costing an arm and a leg and taking up half the living room. It didn't matter how amazing Star Wars Arcade looked when you had to turn your console into a Frankenstein's monster to play it and the competition could blow you away with DKC and Star Fox without needing expensive new hardware. A stronger focus on making great Genesis games instead of trying to turn the Genesis into Voltron would have kept the race with the Snes much closer than it ended up being.