Great idea, mphd168. I don't mind the debate, but I don't like it derailing everything else.
In my opinion, uptown Waterloo is nicer and offers more, for the time being. Definitely better pubs and more of them (only Bobby O'Briens can compete in the uptown scene). Better streetscape and the pedestrian activity goes beyond the typical 9-5 (though Kitchener is busy at lunch). It is better located in terms of being easily accessible to the large student population that lies just to the north-northwest. At present, more development proposals seem to be on the plate for uptown. Lack of panhandlers and sketchy types is nice, but in some ways, it makes it seem less real. The shopping is more high-end, which works for some people, but much of it is out of my range.
Downtown Kitchener has some leads over Waterloo. Mainly, it is larger in geographical size, population, and number of employees/businesses. It is also located very centrally and serviced by a large bus terminal, which is something uptown does not have. Downtown is not completely without nice businesses. Ye's sushi is a great restaurant, and it lacks an uptown location. Catacombs is downtown, as well as Pepi's. Matter of taste has a better street presence in downtown than it does uptown. Downtown has better markets, including the Farmer's Market and New City supermarket. There are more interesting old buildings (though Cambridge has both of the twin-cities beat in this department

) and King has more of a continuous, big city feel when you look down it in downtown compared to uptown. The people presence in downtown definitely has more sketch elements to it than uptown, but again, that's part of the package of being a real city. Victoria Park has more character to it than Waterloo Park, IMO, and Kitchener's got a greater stock of residential neighborhoods around the downtown.
In the short-medium term, uptown has more going for it, since it's at the end of the tri-cities that is the hub of the 'new economy', while it becomes more manufacturing-logistics based as you head toward the Cambridge end of things (though manufacturing is absolutely crashing hard now, which is a big problem for this region, especially Cambridge). However, as land values rise and businesses start feeling cramped for space in Waterloo, I can see a filtering down happening towards Kitchener, which in reality, is not that much further. This is already happening to some extent (i.e. Lang Tannery and other previous office relocations to downtown). And sorry, but there's more to downtown in the way of bones. More hustle and bustle during the day, which needs to be extended into the night. Kitchener's streetscape has made a big leap in the past year, for obvious reasons, and feels a lot less creepy at night now.