There have been several extensive studies trying to settle this argument and Bias on both sides.
Best answer, assuming both sides know how to use their weapon? Long sword.
So it's known neither blade is made for blade to Blade contact, very few widely used weapons are made for that actually but in a fight the long sword has a hefty advantage in that it can actually go blade to blade against a katana (Also assuming both blades are made to their higher quality standards). Even without their edge a long sword is capable of dealing out considerable damage from shear force but a katana may not and their thinner frames mean that blade to blade contact with a long sword can cause it to shatter or be stripped of its edge. This means that the person using the katana will be forced to strike defensively while the long sword can choose their approach freely.
This is also only considering the weapons them self, obviously within their time period their are other factors to consider, armors and disciplines that people normally use to lean their argument in their preferred direction, but this is disingenuous. (that's the word right? I think it is)
Also on your initial statement about in games, I've never seen katana shown as weaker to long swords. Normally I've seen them depicted as stronger and often with higher critical rates.
