So the writers would just have to invent transphasic shields (like how Voyager developed those temporal shields due to the temporal torpedoes). There is no technobable you can't defeat by simply inventing a technobable counter. The problem is not with the Federation technology becoming too powerful - just avoid JJ-style universe breaking technology with no counter or stated drawback and there is no problem. The stories will always survive on the characters, mysteries, and universe building aspects regardless of the name applied to the current "shield" technology.
In most cases, the basic properties of the shields aren't important enough to be stated in dialogue. If they just call the shields "shields" and the torpedoes "torpedoes," there isn't a problem. Throw in a screen that does say the shields are transphasic or whatever, and most of the people who care about that will be satisfied.Your point is well taken, and proof that it would be ridiculous. Technobabble to get around technobabble. BOOORRRIIINNNNGGG.