I do think that, if your vision of classic Nintendo is based on N64/GC software and you weren't into portables, there's two areas in Nintendo's line up which i could see being an issue:
- Rare's output. From the mid 90s to the early 2000s, Rare provided 2D and 3D platformers, first and third person shooters, a racing game, a beat em up, and an action adventure game. No single Nintendo studio provides that diversity today outside of EPD.Some of that is simple logistics and the way the games industry has evolved. Individual studios big enough to make multiple large scale games in very different genres are very er, rare these days.
Greater investment in Retro and Next Level especially might help with this area - Retro have made excellent first-person adventure games and excellent 2D platformers; it's just a shame whatever happened post Tropical Freeze has railroaded them for a time. Next Level's output is spread over a longer period than Rare, but they've covered Mario Strikers, Punch Out, Luigi's Mansion, and Federation Force. Genre and series variety again. If those two studios can handle a couple of games at a time, it would make a real difference.