Unfortunately, not only that - seems that Qsys has a lot of schematic problems.
First of all, there is no distinction between inputs and outputs anymore (?!?), unless you open up the symbol file (inputs are light blue, while outputs are purple). The "new and improved" interface has all the signals on one side, so it's pretty much impossible to distinct inputs from outputs. (SOPC 1, QSYS 0)
Second, there is no distinction between lines and buses (?!?!?). When I use select tool which can be used to draw buses/lines once you're over the connection point, in Qsys it only draws lines, no buses. (SOPC 2, QSYS 0)
Third, the complete symbol for Nios is a disaster - signals on one side only, all the lines/text inside the Nios symbol are overlapping, some text going out of the Nios symbol completely (usually signal names, but also some module names). The signal is completely different than all the other HDL symbols in our design. Good Altera, you've really made the distinction - all the other HDL symbols look great, while Nios looks terrible. Now it's really different, congrats. (SOPC 3, QSYS 0)
Fourth, everytime I regenerate, the ports are randomized, as all of you guys noticed. (SOPC 4, QSYS 0)
Fifth, anyone tried to edit the Nios symbol, so that it would look like something usable? It's impossible! Symbol editor has gone back ages from the previous versions of Quartus. (SOPC 5, QSYS 0)
Sixth, address decoding for custom components is a mess. It was a bit hard in SOPC, well, now it doesn't work at all, thanks to the new merlin address router. (SOPC 6, QSYS 0)
Productivity? Please, this is a joke.
How can someone advertise a bad, buggy, unfinished product? And say it's better than SOPC? Increased productivity? :D They act like they never had a good product!