Halo Wars isn't as well known. You have to think of what they have to do in regards to catering towards the larger percentage of customers. The people on forums? We're the minority, we're the people they know love the series just as much as they do (in 343i's case, pretty sure we actually love it more than them) but we don't bring in the money.
Halo Wars 2 didn't do well, and Halo Wars 1 was ten years ago, which is basically a million years in Internet time. Given that traditional RTS games themselves have largely died, the genre isn't that popular, so thus lower sales.
Same goes with the books. That's why 343i is trying to 'simplify' the story for Infinite and make it more like 'Classic' Halo. They don't want to lean on external media because it's pretty clear that the target audience, the everyday Joe Gamer, isn't buying or reading that stuff. All they want is to rush through a campaign then spend the rest of their time on multiplayer.
SO, to answer your question.
It'll probably be Locke, if they don't kill him off in Infinite. He's a familiar face to Joe Gamer, he's marketable, even if the fanbase doesn't like him. The only other Spartan that ever had traction and allowed us to play as them was Noble 6. Everyone wants to be 6 or Chief, no one wants to play as bLue Team or the Three Stooges. And 6 is dead and Chief will eventually be replaced and Halo Wars and it's characters are so far removed from the wider everything else as to be irrelevant, so it'll be Locke.
Frankly, I'd rather they just shut the franchise down after Infinite. 343i has no idea what they're doing storywise and Halo's original gameplay, what made it popular, is practically antique at this point. The only other choices are to mimic CoD/BF or (shudder) Fortnite. Halo had it's time in the sun and it should have ended with Halo 3, ODST and Reach.