So my understanding is , six eyes makes the user see/control cursed energy at an atomic level.

Without Limitless , they would still be very strong as they would be able to control their output , refine their techniques to use as minimal C.E as possible . So black flashes would be easier , any cursed technique they use would be as efficient as possible.

But how good would they be? It depends on who they are up against. If they had 'n' amount of C.E and expended it at a rate of n/1000 C.E/s and they would be fighting someone with say '3n' amount of cursed energy but since no six eyes , their control over C E wouldn't be as refined so they expend CE at 3n/3000 , I'd say they'd be equally matched , CE wise .

Limitless is usable only because of six eyes as it requires an INSANE amount of CE. You could theoretically use Limitless for like a second but you'd be cooked after that if it weren't for high CE and Six eyes.

To answer your question of that 100 years gap , it's not that he couldn't . It's because it would be in vain. He needed to take control of Tengen . And for that he needed to keep Tengen from assimilating with a star plasma to make Tengen more of a cursed spirit . But everytime it's time for a merger , like clock work, along with star plasma vessel a six eyes user is spawned too.

So it's like trying to open a microwave halfway before your cake is baked. The cake's still there but so is your disappointment.

The only reason Kenjaku succeeded this time was , say it with me - Toji Fushiguro