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I'd say Cortana highly likely had a thing for John. She wants to be real so badly and he's the most badass mofo in the universe. How couldn't she be attracted to that? I've always wondered if Cortana's design in Halo 4 was a hint to that. Trying not only to look more human and feminine, but to get John's undivided attention. I mean she's practically nude so...

As for John, at the very end of Halo 4 when Cortana is 'touching' him and getting mushy, he says, "Cortana, please". Just the way he says it implies to me, either:
1. John knows she feels something for him but he doesn't feel it for her.
2. John is either too scared to get emotional, or he's just so damn hardcore about his duty that he will just never break, period.
Not sure which one is more likely but regardless, Cortana seems disappointed about it. You can hear it in her voice, beyond this supposedly being the end for her.

She's a dreamer and he's a doer. For John he may just never wonder if a deep relationship with an AI is possible or if she could ever actually become a real life form. Doesn't really seem to fit his character. He does tend to keep to himself though, so, who knows?

The big problem is if they ever did get into a deep relationship, it would be damn near impossible to keep it strictly/mostly an action adventure scifi game, and would likely turn into a scifi adventure space drama. That's a very different experience, and Halo 4, which toyed with the idea, was not exactly well received at the time of release. Gamers didn't hate it overall, but they weren't thrilled overall either.