Super neat! Just checked it out now, will use it to churn out a few baddies I need for my next run tomorrow.
Thoughts:
1. Better define what Normal/Tough/Bad-Ass are supposed to mean. You could do this by their largest dice pool and/or average critical dice pool, for example.
2. Give checkboxes that allow us to select optional features for a mook instead of hard-coding it in. For example, cyberware off/on, non-lethal weapons off/on, aspected magician off/on.
3. Summarize the condition monitors into a single number. I record their monitors as "Physical HP: 10/10" and it takes me an extra second to count :-)
4. This will take some serious charting, but allow us to specify max cost of single inventory item. For example, no item exceeds 1,000¥.
5. For skill ranks, don't list them using square brackets []. Since that's typically used for limits (even in your own file) it's a bit confusing. You can just list them without extra syntax, e.g. "Automatics 5" instead of "Automatics [5]".
edit: Noticed that your new version already included some of #2, nice! But if it's only an on/off option it should be a checkbox and not a radio button :-P (the UI designer in me coming out)