I did my masters at UKC and also worked at Reading Uni. The main difference I remember is Reading used Dewey and UKC was Library of Congress, but unless you're into library classifications, that's probably not an issue... Also, either/both could have changed since then. Used the careers service in both, which were pretty evenly matched back then.
It does depend a lot on the course, and that should probably be the main criteria.
Campuses - UKC up on a hill, looking down over the city and cathedral, a view I was rather fond of. Walkable to town (though quite a lot more than 5 minutes), also buses. A bus ride away from the sea at Whitstable and Margate.
Reading - also a nice leafy campus (originally parkland for a big house), though I think they're about to build some new halls on part of it. Town is closer than at Canterbury, but also buses. Both are up hills, Canterbury is much higher and steeper.
Reading is a bigger town, with a bigger shoping centre, if you like that sort of thing. I prefer Canterbury - it's more historic and smaller. Though Reading has a fair bit of older buildings in between the 19th & 20th century growth. Canterbury is prettier. I felt safe walking and cycling round both (though I've since lost my nerve for cycling on roads anywhere.) Reading's got quite a few cycle paths these days, and some are quite pretty.
Preferred the swimming pool in Canterbury, but there are more choices of pools in Reading. This may not be a consideration for you...
Fast trains to Paddington from Reading take about 25 minutes. The Waterloo line is quite a bit longer. It's also got direct trains to Wales, the West Country and up north. That Intercity Cross Country line from Bournemouth to Manchester is v. useful, stopping at places like Oxford & Birmingham. Canterbury has two lines into London as I remember, and while there are those who commute to London - I think it was over an hour - high-speed it was not.
I enjoyed my time in both places and I think you'll probably be fine at either. Which might not be helpful to you, but I think I'm trying to say don't worry too much, as neither is going to be a bad choice. Good luck!