do an 1120S for Sept - Dec, and then a Schedule C for Jan - Aug. That was a pain, and it screwed me over because I bought and depreciated a car in November but couldn't do the full Section 179/Bonus depreciation because the business income was split between the S-Corp and the Schedule C.
You are right that it needs and overhaul, but there are so many tax breaks available to business owners that I'll hang on to that as long as I can.