I do not think BIONICLE G3 needs to be connected to G1. In fact, I would argue that having room for having different versions of established characters is a good thing if it suits the vision. I do not think that having different version of character is bad in of itself. Putting a twist on established character can be interesting. Makuta in particular could be handled in various interesting ways.
Problem with Pohatu is that he is a chracter whose character is defined by his friendliness, and making him unfriendly without proper justification is weird, and not in a very good way. But does that makes any changes to his character feel weird? No, the specific change was bad, not any and all changes. For example, they could have made Pohatu hard-headed, which would fit element of Stone while not turning Pohatu’s entire character upside down.
Below, I wrote examples of how some characters could be rewritten, without it feeling wrong. There are more ways that this could be done.
Characters can be expanded, adding upon an established base.
Gali-Toa Gali always tries to understand the world around her and its inhabitants. As result, she is compassionate and curious. When a conflicts breaks out between Toa, Gali tries to defuse it, for she knows that such infighting could doom Toa’s mission. Gali’s curiosity and hunger for knowledge can sometimes be her fault, as in her pursuit of knowing, she sometimes can forgot caution and fall into danger.
Some aspects of characters can be changed or even inverted, while keeping the character recognisible.
Karzani-Karzani is a mysterious being that was once known as best healer in the Universe. When Matoran were injured so much that they were unable to work, they were sent to Karzani’s realm, where they were repaired and sent back in perfect state. Karzani was so dilligent that he stopped caring about his own health, which led to his slide to madness. Overwork and overexposure to dangerous substances caused Karzani to become fascinated with physicaly altering his patients.
When their Matoran began to return drasticaly altered and disfunctional, Turaga stopped sending Matoran to Karzani’s realm. Karzani in turn stopped the remaining Matoran in his realm from leaving and experimented on them further, trying to create a perfect Matoran. He convinced himself that Turaga were displeased because his alterations did not go far enough, and excepts that all the world will hail him for fixing the flawed design of Matoran. When that ilusion is snatched from him, Karzani will become a dangerous opponent.
And as Sonus said, you can avoid this entirely by making new characters.
