Re: Mega-damage, bit by bit
Depends on the tone of the campaign. Personally I am seeing players making glass cannon characters all the time and just whine and complain if something manages to hit them.
To manage overkill on the added skills levels you just have to put your foot down and create some campaign guidelines ala the rule of x. Also to avoid players characters using called shots on the big bosses, consider adding a power to your game called "alert warrior" or something where the ability gives the characters in question a bonus to dcv only against called shots.
There are ways to make armours very resistant to arrows, consider having master smiths being able to create brigadine and samurai armour that are have extra rpd against arrows.