Ordinary mums and dads investors are a good thing. It reduces the burden of the state when people get to retirement, by increasing the level of assets held by individuals outside of super. There is a benefit to society of doing this. The alternative is to disincentivise investing and having everyone just spend everything now, and save nothing other than super for retirement for most people which is a disaster and what our country is trying to do away with, ie. we are actively trying to decrease the number of people that need help (ie. state pension) when they retire.
However, maybe we do have the wrong system in place, its maybe too advantageous, especially to people with a lot of money rather than helping mum and dad investors. Capital gains are not really income and shouldn't really be included in income tax calculations but they are in Australia, which is partially what complicates things.
I think most on here know I grew up in the UK, they have a seperate capital gains tax rather than grouping it with income tax. It has its only tax free allowance (ie used to be very generous at 12k GBP but has dropped to 3.5k GBP) and its own tax rates. The UK also provides some favourable investments called ISA's where again you have an annual limit that you can put in there, and the returns made on the assets within the ISA are tax free for life (I think the limit is around 4k GBP per year).
Its a much fairer system, essentially in that there are caps on the tax free benefits that you receive, unlike the unlimited tax free discounts that we receive in this country for capital gains. Ie. if you were so lucky to gain $1m on an investment in AU and you held it for more than 12 months, then you immediately get $500k tax free essentially due to the discount, whereas in the UK, you'd get something like $7k tax free. It seems a much fairer system to provide tax free benefits (they also have govt matching on ISA's for those with lower incomes) to more people, whilst capping those benefits for the richest in society.
Whatever system we have, needs to be fairer but also needs to incentivise investing for most "normal" people in the country. Your scenario of removing all benefits probably does the 1st one, but it completely removes any incentive to invest and try and build your own retirement savings outside of super.