Lyric discussion by Lateralus07 

Cover art for Naked Sunday lyrics by Stone Temple Pilots

I think it's speaking of the nature of duality. You can't have light without dark or love without hate. The depths of evil we endure is the very thing that gives us the capacity to feel the peaks of love, and they are kind of one in the same from a certain philosophical viewpoint. Perhaps the "been waiting awhile to meet you for a chance to shake your hand, to give you thanks for all the suffering you command" speaks of some creator who has the wisdom to understand that pain must be experienced to experience love, whereas, the alternative really would be no experience at all.

Alternatively, it could also be interpreted as sarcastic praise of the creator, critisizing the commanded suffering. And maybe the writer believes there is a way to experience love with hate. In truth, I can't say I know.

My Interpretation