Kind of like a union or something. 
lol like a student union...
LOL. I was expecting you to come, guns ablaze, 'it's your choice if you want to do VCE....stuff stuff...if you don't like the rules then you have a choice not to do it...' 

In all seriousness / back on-topic, it is quite harsh that a student should have to sit 3 exams...but what do you propose of those who decide to cheat the system and find out the examination contents for the supplementary exam from their peers? Perhaps we should adopt a system, like at uni, where the supplementary paper is different from the original paper. Of course that will raise questions as 'what if that exam is easier/harder', but can you suggest anything better? That they're supervised until the next day? Heh. Sounds very 1984 to me.
Besides, a person's performance on the exam is based around their knowledge on unknown sets of questions. Is it truly fair to say that an exam is 'easier/harder' as much as it is to say that 'all students will find this exam easy/hard'? Each student comes into the exam room with a different skill set, and so the perception of easy and hard is most likely normally distributed in both regular and supplementary examinations (as are the results, typically). 
What I'm trying to say is, basically, you walk into the exam room with a element of 'luck' (ok, so it's predetermined, but you don't know what's on the exam). You may be weak in some areas, but stronger in others. You don't know what's on the exam paper - you may get something hard, you may get something easy - to YOU. So what difference does it make if a *different* exam was set for these students? From the student's perspective, the exam contents are unknown and 'random'. 
Also, I don't see why VCAA would change their stance unless someone had messed up with their system...or there was reasonable suspicion (and quite rightly so, given it's the VCE) that people were using the extra time to their advantage.