1.9 seems to be using item/generated now as the base model for its items. However, when using builtin/generated, which is how most people made items for 1.8.x, they end up rendering much larger. This even affects Minecraft's own model-missing model, as demonstrated in the screenshot.
I noticed in the code that at least one call to scale by half was removed, and if that's the case in other relevant locations as well, then I suppose that the builtin/generated model is going to have to be scaled itself to adapt to that. Otherwise you're going to have a lot of peoples' custom models from 1.8.x which can't be easily brought forward.
The builtin 'missing model' has no settings at all.