I have a $45 USB dongle with hundreds of dollars of software licenses on it. It plugs directly into the USB port. That is my [u]least[/u] [u]favorite[/u] [u]feature[/u] of that device, and I'm talking about something that imposes DRM here, so there's plenty to dislike. After the third time of it getting snagged on or crammed into something, the plastic started to crack around the USB plug, which was also bent at a 15-degree angle. So I soldered a 1ft USB cable to it and wrapped it in electrical tape.
Protruding from the case is OK for my Logitech wireless receiver, because it's all of 3mm deep. Not OK for a device that sticks out more than an inch, IMO. That's just begging for loose or broken connectors. Not to mention the usability aspects. a 10' USB A to USB B cable is far easier to locate than a USB A Male to USB A Female cable.
Look, use what you want. But this "mine's superior to yours because of this aesthetic detail" nonsense is ... nonsense. My preferences are clearly different than yours, and that seems to be the case with others here too. So "better" is not an accurate description. You're not cutting edge, you're just different.
Finally, 6-pin ISP is, I believe, far more prevalent than 10-pin ISP. The latter is a nice bonus if it's there, but the 6-pin variety is an absolute requirement. Say what you will about the Uno, it's the gold standard, and not supporting it and the whole "shield" concept (irritating as the pin header offset might be...) is a poor choice when compatibility with unspecified user equipment is of any concern. (Of course, on your own systems/projects, do whatever you want for an interface.)