I agree--it would be better if G2 stayed a reboot. I've thought a lot about how the story team might go about a "continuation," and the only idea that I've come up with that really works isn't even a continuation at all really...
I suppose that if the story team wanted to make a tacit link between the generations, they could do it like this. Okoto and the G1 universe exist in separate, parallel universes. An indeterminate time after the Reformation of Spherus Magna (as in, it doesn't really matter how long afterward, 'cause we have no story for that time), the denizens of the "Okotoverse" needed the Toa to defeat the Skull Spiders. Using the Mask of Time from their universe, they summoned the Toa from the G1 universe, giving them new forms. Presumably, in this idea, the Toa will eventually learn that they originated in a different universe, and may--at the end of the story--return to the G1 timeline.
That's the only way I could see this working. Anything more integrated will cause continuity issues with the old universe (i.e. saying that the G2 Toa are the G1 Toa before they arrived on Mata Nui, which we know is false) and anything less integrated is basically just a reboot (i.e. Mata Nui exists in the Okotoverse, but is different from the G1 island).
I just can't see an easy way to make everyone happy--not that I think LEGO should try that.