Not necessarily a scene, but I feel that he and Morpheus would have had a stronger father / son aura. And yeah, a lot of that relates to the shared race and physical appearance between Will and Fishburne.
They would have had to recast Trinity. Will and Carrie-Ann would not have chemistry.
Overall, Keanu did fine. But I do think Will would have done well too.
I don't think it would have had the same tone. I mean I think he can be a good actor, but I just can't see him pulling this role off. His style is loud and obnoxious while Reeves' is calm and reserved.
Would have been a completely different film and probably not as good. At the time, he was also Agent J from Men in Black, and it would have been hard for fans to envision him as Neo without also seeing agent J (who also wore the black attire with the sunglasses)