Agreed. After having used the new station for a few months, I do have mixed feelings. It's obviously a vast improvement on the old station, in terms of aesthetics, passenger flow, and most importantly, enabling frequent Thameslink trains. And I appreciate that the design will inevitably have been a compromise, limited by cost and also by all sorts of restrictions on what could safely be done - which most of us would be unaware of. But even so, I'm starting to get impression that the design perhaps emphasized aesthetics too much over passenger convenience.
One thing that strikes me is the vast height difference between the concourse and the platforms. Makes the concourse look amazing, but also means passengers changing trains have to go up and down unnecessarily large distances. This adds to the time to change trains, and means lots of people who would normally use stairs head for the escalators or the lifts instead, somewhat restricting flows off the platform. I'm also going to join the 'one lift per SouthEastern platform isn't adequate' brigade: A few days ago, I used the lift because I had my bicycle with me. Off=peak, mid-morning: Took the lift two round trips to accommodate everyone off my Cannon Street train - by which time another train was already disgorging more people into the queue for the lift.
I do wonder whether it would have been better to provide a balcony (Waterloo-style) or an overbridge so that people changing trains wouldn't need to descend all the way to the concourse and back - this would have had the side-effect of reducing demand for both the escalators and the lifts.
Then there's the location of the concourse even further from the Underground (where many people would be heading) than the previous concourse - although granted, the existence of the Shard would restrict what could be done there. Given the distance, did noone think about providing travelators, similar to the one between the Jubilee and Bakerloo/Northern platforms at Waterloo?
Lack of toilets inside the barriers is also an issue, although it's nice that there are ones outside the barriers.
Don't get me wrong, I'm not sorry that the station was rebuilt, but I do wonder how much of a priority passenger convenience - in particular, minimising the time for passengers to get between platforms/underground/exit/etc., got in the design.