Regarding our penises...
You're absolutely right that the downside of having external genitalia is the increased vulnerability to pain inflicted (to our anatomy) by external sources.
But, if you put aside the men who compare penis size/shape/cosmetics in order to try to gain superiority or the "upper hand" over fellow men...
It also can be a real point of bonding. In healthy male friendships (or even acquaintanceships), we almost instantly "get" each other on that primal level. You can just refer to the benefits/hassles/pride/drawbacks of our penises...and it's sort of like a silent "nod" of brotherhood that doesn't even necessarily need to be spoken.