How to make public transport worse

Amsterdam has a metro-, tram- and bus-system. Like many other cities, there are no single (point-to-point) tickets. The cheapest fare is EUR2.80 for 1h of public transport usage. When you buy a ticket you have to activate it by ‘checking in’: Swiping the more-than-plain-paper ticket in front of one of the ubiquitous readers. A double beep and a green light signal that you a cleared to go. No problem with that, if you don’t mind the delays when 10 people try to get onto a tram through the same set of doors.
When you get off you have to ‘check out’: Swipe the ticket in front of one of the readers, beep-beep-green light and off you go. Same routine for each and everyone on the metro, tram or bus. If the check-out does not work or you simply forget to check out, your ticket is invalidated--no matter whether it is a 1 hour ticket or a multi-day pass.
While the readers for the metro are located of the platform, for the tram the readers are located inside the carriage. In order to make sure that their customers are actually checking in, you are only allowed to enter the tram on the front and one of the hind-doors. In the front the checking in is supervised by the driver, the hind-door is supervised by a conductor sitting in his own pseudo-booth. Even though you should not exit the tram using the entry doors but should use the exit doors only, all the readers let you check out and patrons use all the doors to get off the tram. Because of this public disobedience and the delay introduced by the mandatory checking out procedure extra stops had to be introduced at busy stops, e.g. Amsterdam Centraal: The tram halts, nearly everyone gets off, the doors close, the tram itches forward one tram-length and stops again for boarding.
You have to enter the bus using the front doors, check in and leave via the hind-doors. No problem if the bus is more or less empty, but very ‘time-consuming’ if the bus is full and the distances traveled are only a few stops. And, don’t forget to check out!

The problem with this modus operandi are twofold: Why does not 'checking out' invalidates a ticket that is time-based? Did anyone address the obvious privacy concerns? It does not seem too bad with short term tickets, but the same rules apply for longer term tickets as well as personalized chip-card based tickets.
Is the extra information gained by sampling traveling profiles, i.e. knowing entry and exit points of all passengers, really worth the effort, the privacy concerns, and the delays in service and inconvenience to one's customers?
If I had a choice I would not use the system.