He fuck them all
Ohh spoiler
He choices all of them ٩(๑❛ᴗ❛๑)۶
If you are *really* only interested in the juicy stuff (which I think is a pity), skip to chapter 82.
spoilers
The real resolution is a bit difficult to grasp (see my rating notes). But he eventually chooses all three of them and after some chaos they all end up staying by his side. In fact, near the end there is even one additional companion though not yet physically since she is still too young. But it's pretty clear that's just until she's old enough ^^
I don't know who ended up with Nagi-kun... I was reading upto ch 51 and I just skipped straight for the last chapter and I still don't get it but its a nice manga..