I don't have a problem with using USB hubs. My 2012 MBP 15" has only two USB-A ports. But my USB peripherals have always outnumbered the onboard ports on my home desk, because I always use more than two at a time. For example, I always have at least a time machine HDD, audio interface, webcam, and wired mouse at my desk. So at my desk, I have two powered USB3 hubs (4 and 7 ports).
For my coming MBP16", I also ordered a thunderbolt dock with USB3 ports, and will plug in my existing powered USB3 hubs into it. No problem.