He may be able to present options that allow you to defer capital gains taxes that you hadn't thought of.

Looked at a property in Little Village yesterday at 95k but it needed a full gut rehab and a lot of deferred maintenance exterior wise.

Distressed properties, lots of deferred maintenance. 

Is there anything besides deferred maintenance that might increase/decrease the reserves you set aside?

I'm no expert on them but thats a mechanism for trading up and deferring capital gains taxes.   

This was the result of a leaking pipe in the laundry. 6 months later, no mold has returned, but I still have several areas where the idiot painted directly over the mold that I have deferred fixing until I'm ready.

Plus I contribute 20% of my salary to a Tax deferred annuity... are these things that would also determine whether a Roth or traditional would be better?

So the exit strategy from a live in duplex is that you'll get some of the gain tax free and the rest of the gain will be tax deferred. 

I have a full time job and will invest in real estate to grow net worth, provide a little cash flow to retire in 10-12 years, provide a little tax deferment on investments, and some diversification outside of the stock market. 

We began as a company and as individual investors to make this switch in mindset about renovatoins and how to renovate at the beginning rather than deferring mainenance in 2011.