Mikeal and Lisbeth's separation is designed specifically to make you want them together again, to create build up and anticipation of seeing them again. This is a repeated theme throughout the trilogy. They're not meant to be typical partners or lovers. I think this is what makes their relationship so unique compared to other literary and cinematic couples. Both of them end up cherishing their friendship but both are acutely aware that they wouldn't be a very good couple despite their obvious feelings for one another.