Tbh I feel like more times than not Nintendo hasn't had a great track record with console transitions. A big problem they'd typically have is taking too long to release their consoles, mostly cause the software teams weren't prepared to transition quick enough to the next console.
Imo I think Nintendo took a bit too long to transition from the NES to SNES cause it gave Sega a critical 2 year headstart where they were the by far the most capable system and allowed them to eat away Nintendo's marketshare early which set them up to compete even after the SNES released. Had the SNES released a year or 2 earlier, i feel like most people wouldn't have given Sega a 2nd look since Sega wouldn't have any major advantages over Nintendo to choose them over a well known brand like Nintendo.
Nintendo also took too long too release the N64, it was supposed to release late 1995 but again due to software delays as a result of its hardware being overly complex is got pushed to 1996. This gave the PS1 a 1-2 year headstart as being one of the only good 3D consoles that, by the time the N64 released the PS1 already had hundreds of games for the same price which made PS very enticing. Nintendo especially failed with this hardware transition not just cause they launched later than anticipated, but focused too much on specs rather than ease to develop for which is the reason why the N64 had so many huge software droughts from both 3rd parties and even Nintendo, and imo this decision to use complex hardware would hurt Nintendo going into the next hardware transition.
The GameCube also took longer than anticipated to release, Nintendo was determined to get the system released by 2000 to not give the PS2 any headstart but failed again since the software wasn't ready. Since the software teams were taking so long to produce N64 games on the complex hardware, it took longer for them to transition to creating games for the GC and based on what it seems it sounded like Nintendo's software teams didn't really want to transition from the N64 since they were just getting the hang of N64 hardware towards the end of the generation, they just felt sort of forced to transition. Even with the 1 year delay of the GameCube, after launch the GameCube had such a quiet and poor first year for the console when it came to games to the point where they rushed games like Mario Sunshine just to get games released in a timely manner. Nintendo definitely could've handled the transition better.
The transition from the Wii to Wii U could've been handled better, Nintendo was unprepared with HD development which took them much longer than anticipated to get a good release schedule for its first year.
Imo the best hardware transition has to be from Wii U to Switch, even though the Wii U's life was cut short, it still feels like Nintendo gave it a proper ending giving it big releases like Mario Maker, Splatoon, and Zelda BOTW to end its life and Nintendo was completely prepared to launch the Switch with one of the greatest first years of a console ever when it comes to games, a new 1st party game was release at a rate of nearly 1 per month, its one of the big reasons why the Switch succeeded so early.
