And the lack of a easy to enable/disable automatic board reset via DTR signal. Over complex/designed auto voltage switching Vs simple manual switch or jumper.
All these have been discussed forever on this forum, so it's a bit old in the tooth. Plus one can always choose 3rd party boards that correct or improve some or all these 'problem areas'. Still all in all the Arduino platform has seemed to have become the dominate hobbyist platform at this time inspite all it's 'flaws', so many of us have tired of the subject and have moved on. 
Not sure I'm too impressed with the new Uno board with all it's various bootloader bugs to date, ceramic resonator Vs crystal, SMD Uno model without the removable 328 chip, but then again I don't have to buy one do I?
Lefty