One thing to keep in mind is that certain skills get more or less powerful depending on how advanced the recipe is. For example, Ingenuity and Ingenuity II are very powerful for 1* and 2* recipes (starred recipes are the "advanced" recipes for a class; they are listed as level 50 or 60, but are actually much more difficult than level 50 or 60 recipes are, and get more and more difficult with each star), but their benefits drop off sharply when used for 3* and 4* recipes. Piece-by-Piece, on the other hand, becomes MORE powerful for higher star recipes, as they continue to complete 1/3 of the progress even though the progress bar is much longer, and the potency of Synthesis steps is lower.

I'd hazard to say that EVERY level 50 cross-class skill has a use at some point, a moment where it shines. Part of the fun of solving the great crafting puzzle is figuring out when those moments are!