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If you want to design with lots of Altera IP modules, and just have them wired together, with a bit of your logic, then Qsys/PlatformDesigner is a reasonable way to go.
However (as I do) you tend to use very little (if any) of the canned Altera IP modules, then Qsys/PD is basically irrelevant and provides no real added value.
So it depends on what you are trying to do, and how you plan to do it.
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I don't know if I'd totally agree with that.
Even if you don't use Intel FPGA IP, you can create your own custom components and connect them together, relying on the interconnect automatically created by PD instead of building it all yourself.
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