It seems to be pointless to compare a unit like the mercy to other bombers. It is very unique in the way it attacks. Single pass, 100% accuracy. It is very unique in its weaknesses: Very low HP, low fuel. 3603 basically removed the second weakness, since now the mercy has plenty of fuel to fly around most maps that are played.(you can snipe opponents mexes on setons now)
The very low HP weakness only works when it actually gets shot. If the mercy isn't shot because the opponent had no units to shoot at it with, then there is no discussion. If the mercy doesn't get shot because t1 and t2 flak miss, it becomes interesting. This is precisely where the discussion should take place. Not a very broad discussion about the game in general.
Is it ok to have a unit that has t2 cost, comes in at the t2 stage, has very effective and unique attacking attributes, and in some CHANCE cases no weaknesses. I think the main point here is CHANCE. It is possible to gamble with the mercy because counters besides t3 air are never 100% effective.