I agree it's likely to be Rubio vs. Hillary in the end.
However, if Cruz doesn't drop out, then it'll make Rubio's pathway to the nomination more difficult.
Rubio needs to cut a deal with Cruz so Cruz drops out.
For example, Rubio could offer Cruz the VP or SCOTUS nomination. The big problem though is VP and SCOTUS nominations will be difficult for Cruz. Cruz as VP won't necessarily help Rubio and in fact it might even hurt Rubio to have Cruz as his VP. SCOTUS is more of a natural fit for Cruz given Cruz's resume, etc., but Cruz will likely struggle to get the SCOTUS nomination because his own party hates him and he might not be able to get enough of his own party's Senators to vote for him even if Rubio nominates him.
The bigger point is that Cruz needs to drop out, and the sooner, the better. Otherwise if Cruz stays in long enough, he'll keep dividing the anti-Trump votes in his party, when the Republicans need to consolidate all the votes if they don't want Trump and/or a brokered convention. But what can motivate Cruz to drop out?
Or we could just watch it all burn, which might be even more interesting.