1. remove these tax preferences.
if we wanted to retain some of the incentive for startups, we could phase out the tax benefits based on the valuation of the company at time of grant. so a grant of stock options for a $1MM startup might grant you a tax preference, but not for a (mid-sized) $100MM company. (however, phase-outs need to be continuous functions to remove the gaming potential, and politicians hate that.)
2. remove the tax advantage of debt
3. remove carry-forward/-back losses
4. remove the separate capital gains/carried interest rates and all related exemptions (like 409's)
5. remove accelerated depreciation/amortization
and more. in short, remove tax loopholes, thereby dramatically simplifying the tax code.