I think there are a lot of potential challenges the Surface is going to face against the iPad Pro. While I don't see the Surface/Surface Pro and iPad filling the same needs I think the way they are priced is going to make people compare them.
The first challenge is going to be the SP4 vs the iPad Pro. Assuming they both come out around the same time and are both priced around the same will we see more iPad Pro sales or Surface Pro sales? To me this is going to be an indicator showing which company consumers prefer. Windows has always been the top in desktop OSes, but Microsoft stands to lose a lot of face and confidence if the iPad Pro with iOS outsells the Surface. It's going to mean that despite price people prefer Apple and that could damage Microsoft. It will show that Windows greatest strength doesn't really matter anymore. If the Surface Pro sells better then Apple will start feeling the heat as it will show people want a "real" OS on a "Pro" device.
The second challenge is developers. If the iPad Pro sells more than the Surface it's going to confirm developers' belief that iOS development is the way to go. Yes there is the iOS bridge, but Windows will take a back seat. Why I think this is a big challenge is because if you look at app development today much of the mainstream and exciting stuff is happening on iOS/Android. Windows development has been on a downturn for a while. People argue that Windows still holds the mighty desktop share and the ability to run "real" apps like Photoshop... but those are older apps. When is the last time anyone was really excited about a new Windows desktop app that is not a game? In recent years we have seen the iPad get many non game apps that would have normally been made on Windows. Flight apps, graphic apps, learning apps, scheduling, mail, media, etc. Apps are no longer simplistic programs just for phones.
If the iPad Pro sells well developers could jump on board to create more powerful desktop class type of apps on iOS. Eventually even apps like Photoshop could find themselves competing against apps on iOS and there wouldn't be a huge disparity in feature sets.