In all honesty I like the update but I prefer the command input of Tower 2011. It seemed more intuitive. E.g. Before, you would say taxi to runway 25L but now it's simply runway 25L. I generally like to micromanage the flights so I will send them to the runway, ask them to line up and wait then give clearance for take off. In Tower 3D I have to say the runway before each command : "XXX runway 25L, line up and wait" then "XXX runway 25L, cleared for take off". In Tower 2011, you could just give the command "line up and wait" or "cleared for take off" without having to restate the runway each time. A minor niggle. Same for landing. You have to say "Runway 25R, cleared to land" even though you issued the "Enter Final" clearance to that runway a couple of minutes ago.
Also, aircraft hold short of runways without having to issue that specific command. Maybe that happens in real life but I'm just used to the old way of Tower 2011 where aircraft continue their taxi unless instructed.
These are my personal observations and new players to Tower!3D won't even notice them but I just liked the feeling of squeezing departures and arrivals close together and being able to issue truncated commands added to that ability. Maybe the devs could make a few changes and offer options to issuing commands. :)
I hardly look at the airport view of Tower2011 or 3D view of Tower!3D so to me issuance of commands is the major deciding factor.