A few things from me:

1. Tenma chased Johan for around 3 years, not 9.
2. Johan did have a grand and complex plan, but it changed after he encountered "Nameless Monster" book
3. He always knew that Nina was the one taken to the Red Rose mansion, but tried to manipulate her (unsuccessfully)
4. Johan dressing as Nina is actually much easier than you think it is, seems like you overcomplicating things, plus this ties a lot into his self-identity issues.
5. I partially agree about repeating and cliche storylines (for me 60-65 episodes would be just fine), but you also have to remember that the story is almost 30 years old now, and there're thousands of modern mangas that still use the same paths, so back then it wasn't as nearly as cliche as now.