I'd like to make a comment in general about the whole 'prestige' and 'reputation' thing - most undergraduate degrees have to follow the same (or extremely similar) course programs in order to receive and maintain accreditation from professional bodies (e.g. Engineering has Engineers Australia as their professional body, Australian Computer Society for the CompSci/IT areas).
What you'll find is that most of the content is extremely similar - yet what makes unis stand out from the rest is the
way they deliver this content (this is broad, meaning the quality of the lecturers/tutors/demonstrators, quality of the extracted content from the prescribed textbook, and so on). I've been fortunate enough to experience both La Trobe Uni and Monash Uni (you can
arguably say that they represent two different 'prestige' classes - so to speak). Honestly, I don't see
much of a difference between the two.
When making a decision about your future university,
please don't take 'prestige' into account (or if you do, make sure it isn't the primary reason).
However many inside my school, say Monash is better for science, Deakin has a better atmosphere and there hasn't been many commendations of Melbourne.
What you have said here is true. Each university has their pros and cons - this is something you need to think about. I personally think that the only way you're going to know for sure is by
going there and finding out for yourself. There are always options to transfer after 1 semester if you don't like the culture or programs offered.
Just needed to say this. Cheers.
EDIT: In terms of my personal experience with Melbourne University, I applied to be part of their MTeach program and didn't get in for whatever reason (but got into Monash, which is good). Anyway, I tried to contact the graduate school responsible right after the offers came out just to get an idea of why I wasn't accepted (because I wanted to know). To this day, I still haven't received a reply from them. They're meant to be this professional, prestigious university, yet can't take a few minutes out to respond to an email. This makes me glad that I got accepted into Monash because I couldn't be happier now.