And I was hoping to avoid that question by the clarification. Not because I haven't thought of it, but rather because it is somewhat tangential to the issue itself. Still, to answer.
To me, who would win largely depends on the circumstances. If Diana suddenly appeared in Gotham and attacked Batman by surprise, of course Diana would win, with Batman's only hope being that of escape. On the other hand if Batman knew the fight was coming and had time to initate one of his many plans, then it could easily go to Batman. To me one of the central themes in Trinity, besides their symbolisms and all that, is that they are all credible threats to pretty much anyone, with their own strengths and weaknesses, and it is that balance that drives. It also means that any one of them should be able to defeat another one if it comes to that, otherwise it pushes one of them higher than the rest. Whetever or not one likes it, the fact is that Batman has been established as the ultimate strategist of DCU, being able to locate and exploit the weaknesses of much stronger opponents. This is why he was in the Morrison League and why he belonged there. And to pre-emptively answer the question of how someone doesn't like, that in turn is a matter of opinion, which is another discussion.
To continue, if there was a fight between Batman and Wonder Woman, for whatever reason, in truth I would be okay with either of them winning, especially if it didn't take place in their individual titles. The more important fact to me would be that both would come out looking good and with a feeling the fight could have in the end gone either way.
Does that answer the question to your satisfaction, even if you do not agree?