If you buy in your company you lose the 50% CGT discount. Also, if you do decide to keep some or all of the properties you may want to later transfer control to a smsf which you can only do with certain types of trusts. Take a look at the different trust structures (not a family/discretionary trust) to see if you can achieve the immediate tax deductions anyway (see the 'how to' guides here (they use macquarie deeds) http://www.investorone.com.au/index.aspx?p=trusts )

If you disagree with your accountant or feel he isn't giving you the info you need for you particular situation why don't you set up one or two meetings with an accountant who specialises in property investment. He should tailor his advice to your circumstances and goals and answer all your questions accurately. You could save yourself a lot of headaches by getting the structure right upfront rather than trying to make an educated guess and not necessarily knowing all the variables (for example the cgt thing).