Well, I do remember a Master System II and a Mega Drive 2. So I guess they just didn't think far enough ahead and ended up having to change the name because they'd already used up the "2".
I remember that long before the 32X and Saturn were even announced, there were rumours of SEGA working on the "Giga Drive", but I'm glad they didn't actually go with that name. It doesn't sound quite as good, and the further you progress, the sillier it sounds. I just can't see a "Yotta Drive" having any success as a game console.
The fact that they released it as "Genesis" in the US didn't help either, of course. That would have made the Dreamcast the "SEGA Leviticus".
I somehow doubt "NES 2" would have inspired the same desire in nineties kids as the "Super NES" did. Mega Drive was already an established name by then, and Nintendo knew it. They needed a name that sounded just as powerful. But of course it presented the same problem when naming their next console. There isn't really a step above super (which in itself already literally means "over" or "above").
The Wii was sometimes mockingly called "GameCube 2" because it was basically the same hardware with a few upgrades. And the last time Nintendo did try to stick to their home console's brand name with "Wii U", it was a decision they came to regret.
I guess the only way to do it right is to do it from the very beginning and stick to it, and you've got to hand it to Sony, they did just that. People can already dream of a PlayStation 5 or 6 even today, while all the other brands' future console names are (almost) completely in the dark.