I think a lot of posters on here have forgotten that a completely new schedule will be flawed slightly, but as with all other timetables you are used to, this will iron out eventually.
As for the increased journey times, that's obviously a reliability measure. I can understand a few minutes extra can be irritating but obviously you would rather your train arrived on time and not late. The network has become more congested as a result of increasing passenger demand so dwell times and running times cannot be as short as they used to be without jeopardising the robustness of the timetable.
I think for the most of it, the new timetable will bring a lot of benefits regardless especially on the ThamesLink front. A new train timetable will mean a new commuting timetable for everyone, hence the loud hurrah about it. But take my word for it, things will get better.