Yes, the cases should become more complex and possibly require more travel or thorough investigating. I can only image what mindfuckery that ensues down the road. If we wanted to run with a lost pet, we could suggest other pets have been going missing, hence it's not a typical 'ran away' idea, as much as someone is taking them for some reason. And yes, Moriarty and Holmes will surely end up clashing with their massive egos, though that's not to say that once Moriarty appears to have lost, we wrap things up. Other larger scale cases can surely be had.

What I mean is, I don't see the endgame being that easy or final.

Irene is bound to turn against Moriarty though I see it happening much later. I don't think she'll suddenly see the picture clearly for the world, as much as, it's for her own good if she is no longer around such a crazy guy like Moriarty. I would assume for now, she's on board willingly because of money? I would assume later, it would become blackmail? If she's still a wanted thief, that might be enough to hold her loyalty until a breaking point. Of course, there's also the inevitable reveal to Mary and the others that she was on Moriarty's side, which I'm sure will be good fun to play out too. It would be interesting to have her keep switching alliances, since I see her as more of a selfish person who wants to be safe and well off, but should she come to really care about Mary, John and Sherlock, that will be interesting to play with as well.

We have some good complicated dynamics set up which is very exciting.