The term "transphasic" applied to the torpedoes, not the shielding, which was just called "armor."
And the "Endgame" armor -- often nicknamed "Batmobile armor" -- is, quite simply, a stupid idea. There's no good reason for using it. It's heavy and ponderous. It would reduce the ship's maneuverability, and it would block the ship's ability to radiate excess heat, thereby eventually cooking the crew inside the ship if they used it too long. (Contrary to the "space is cold" assumption, vacuum is a superb insulator, so ships are at more risk of overheating than freezing.) And when you're dealing with space battles involving high-energy plasma weapons, thick armor would actually do more harm than good, because high-energy charged particles striking a dense armor material will actually create more deadly radiation
in the form of x-rays. So far from protecting the crew inside, dense armor plating would basically doom them.
The only credible reason why they used it in "Endgame" at all is because the Borg hadn't seen it before and thus wouldn't have adapted to it -- but the reason they hadn't seen it before is probably because it's so damn stupid
that nobody would use it for any other reason.