If we're going to do mysteries I think we should do them right :) Make the crime itself petty, but within the crimes leave a sort of pattern, a clue to hint at something bigger. Knowing Holmes he'll almost obsessively chase after them, and Moriarty can get him believing/doing what he wants for a time most likely. It'd be a lot of deceit on Moriarty's part, which coupled with Irene's help will definitely through our pair through a loop.

At most I would say Irene could share her thoughts on cases, and let Mary do the helping. Again, as I said it'll be more a case of careful manipulation to have Sherlock, Watson and Mary doing what they want without directly influencing them. That is too of course if you think that's a plausible idea.