Is there some reason we're looking at this as an either/ or kind of deal instead of an and type situation? In other words, what's the numbers on a Focused Proton Torpedo strike?
Also, as I've only just found out tonight reading the rules questions forum here, being secondary weapons, PTs wouldn't gain an extra die at range 1 (not that you can fire them at range 1 anyway, of course), however what had eluded me is the fact that if you fire PTs at a ship range 3 away from you, they don't get the extra defense die for the same reason.
Action economy. Using a proton torpedo takes an action that could have been used to do something else. Comparing a Torpedo that takes an attack and an action to a primary weapon attack with no action would be meaningless because they aren't the same. Also remember that target lock and focus have the same effect when treating crits as normal hits. Yes, the Torpedo also requires a card that costs 4 points, but that decision was made even before the game started and doesn't effect the action economy.
Regarding your second point, I accounted for the in my last set of charts.
Torpedoes suck on X-Wings or any other ship with a 3 dice primary attack. They aren't too bad on Y-Wings (especially Horton), but that is about it. With all the new ship upgrades, there is no reason to use them any more.