I should preface this by saying I gave my thoughts if I were to be pushed on who was more likely--as I said, I'm fairly 50/50 on them.
I feel like they're both very comparable in terms of popularity in Japan--one could argue one is slightly more popular than the other (I've heard it go both ways), but in comparison to other candidates, they're both virtually non-existent there. I mentioned the history with Nintendo as a factor was in comparison to Halo. While the character of Cloud was less associated with Nintendo, Cloud was there to represent the franchise as a whole, which did have a history with Nintendo. In comparison to Doom, Halo as a series has no relationship to Nintendo currently, and there's only a theoretical connection with a possible MCC coming to Switch. That being said, even if it doesn't come to Switch, Master Chief is still very possible in Smash. I gave the example of Joker. That Nintendo went with Joker, rather than a character from Shin Megami Tensei, demonstrates a bigger deviation from having characters/series with strong ties to Nintendo.
Which is why I noted it as an exception. So, Master Chief could be that exception, and if he's in, I'd expect him to be the first or second character in the pack, as that surprise character. But I generally stray away from thinking of who that exception would be, rather there will be a surprise character. Could be Master Chief, could be Sora (since most dismiss him due to the Disney connection), could be an assist becoming playable, could be a character I'm not even considering at the moment. If asked if Master Chief is possible, I have no doubt it's possible, especially given Nintendo and Microsoft's growing relationship. It's when asked if it's likely, that I feel less confident about. I suspect there will be either no Western characters, or at most one, and there's plenty of candidates.