I don't really mind the long "use" steps all that much honestly. Yeah they take a long time, but the practice you get is proportional to the duration a transformation takes. So a long "use" step means lots of practice. Yeah, it could be better but it's not awful.
Combinations are really bad. SOOO many clicks and no practice to show for it. My wrist starts to hurt sometimes if I combine a couple stacks.
Couldn't the problem be solved without modifying the UI by just adding new transformations for the particularly tedious combinations (like tea brewing) that have 10 times the ingredients and spit out 10 times the outputs? I mean yeah that's a lot of database work...
Another option would require changing the code I think but it would be more elegant. Presumably when someone clicks the "combine" button there is some code that checks whether the ingredients form a valid transformation. More code could be added to see, if you divide all the ingredient quantities by 2, is that a valid transformation? What about 3? 4? Etc. Maybe up to a maximum (say 10 at a time). If it finds a valid recipe, it remembers what the multiple was, divides the ingredients by it, does the transformation, and multiplies the result by it.
The checking could be made faster if you only allow certain multiples (say 5x or 10x).