I don't get this choice? If I want a road aero frame I'd choose between various models from different manufacturers, and similarly if I wanted a light-weight climbing frame. The intended use should determine the options, not a common manufacturer (unless I only had one manufacturer's frames to choose from of course).
In this case I think the resulting two finalists would for a lot of people end up being the same regardless. Both best in class (aero or climbing) arguably come from the same manufacturer. I'm not into the whole aero thing for my own reasons, but if I were I'd be hard pressed to look further than the Madone. And even though the Emonda SLR is simply too light a frame for my liking, it's the only superlight frame that I would even want to try, simply because I believe Trek to have the R&D resources to pull it off as well or better than anyone. Lastly, the geometry is one that works very well for me, that may or not be the case for someone else. So yes, these would be my two finalists even after looking at all the offerings from all the other manufacturers.
Bingo, Calnago nails it. Trek has two of the top frames in their respective categories. If one wants a lightweight climbing bike, the Emonda SLR at $3000 is hard to beat. Same with the Madone and its aero category. While some might not like the integration, its use of the IsoSpeed design puts it at the top of that category.
Not to mention Trek's offering of H1 and H2 fit means most riders can get the exact fit/very close to it that they want. Plus ProjectOne ability to get a unique paint scheme & Trek's lifetime warranty. Many aspects make Trek a very solid consideration now. So I could definitely see one narrowing down their consideration to either the Madone or Emonda and trying to decide which of those two would best fit their riding. Trek has definitely moved back to the cutting edge of the industry with their engineering and composite layup schedule.