Transphasics, obviously, would have very little inverse shield ignoring, and probably a low-ish amount of shield puncturing, in my opinion. That straight 40% would be your benefit. You can fire it at a ship with high shields and /know/ you're going to get damage.
That's also a good idea! Perhaps some combination of both for the various types of torpedoes, even? That would certainly keep some competitiveness in the works.
I've actually come up with a sort-of answer to the issue of how to make torpedoes a little more competitive... Why not give them a certain amount of shielding they can punch through, IE, if a torpedo can punch through, say, 500 points of shielding, and someone's ship only has 300 in that facing, the torpedo goes completely…