I've been thinking about the
>Knuckles shouldn't be involved in plots that don't involve his guardian duty
>Knuckles isn't allowed to go around and interact with people due to the Master Emerald
Catch-22 problem recently, and I think I've come up with a solution: just expand the scope of what his duty entails.

I remembered how, in SA1, the Master Emerald acts as a sort of out-of-context screen, showing Knuckles images of things it wants him to check out, like the Egg Carrier. If you extend it to act in more mysterious ways (or even use Tikal as an intermediary), it can give him reasons to go out into the world more often to accomplish things that he might not fully understand but is resolved to figure out, and run into the rest of the cast in the process - without sacrificing his central conceit of primarily protecting Angel Island.

Moreover, to tie in with his Treasure Hunter side-gimmick, you could have him seeking out ancient relics to take back to Angel Island for safeguarding - Echidna remnants, symbolic valuables that could otherwise be mistreated, or powerful items that would be abused (like trying to keep the Chaos Emeralds in their shrine every time they scatter). Besides "reasons to be there", they're also perfect points for casual conflict, for things like his squabbling with Sonic, the treasure hunting rivalry with Rouge, or butting heads with good guys over how to do things for the occasional boss fight.