My husband goes from W-2 to 1099 on a regular basis. The downsides are that for the kind of work he does, he gets paid by the "job" so if work is slow, there is less $ coming in and because it's not at all steady, it's very hard to predict his income. But if the money is gravy on top of your wife's salary and benefits, that might not be an issue.
Honestly, you're supposed to pay your estimated taxes quarterly but we never do. If you're married and filing jointly and your wife has taxes deducted every payroll, the IRS seems to not care if you settle up your share at year end, as long as your taxable income isn't huge. My husband is a terrible record keeper. His mileage is always an estimate and his 1099s and actual deposits never reconcile at year end. His cell phone is easy, it's just a portion of our monthly basic cell phone bill. Ditto the home phone as we need the land line for him to send and receive taxes. He deducts office supplies, computer hardware and repair, and because he works out of our house, 1/6 of our mortgage payments, taxes and utilities (his "office" space is one of the 6 rooms in our house). He does not deduct meals because he doesn't take clients out.
We have an accountant who does our taxes. He works with a lot of 1099 clients and his take on things is that if you get audited, then you get all your ducks in a row (put together a mileage log, etc.). My husband is honest with his deductions, just not meticulous so I know that everything he deducts for the business is valid and could be justified if need be. Mileage is probably the biggest pain - if I were on a 1099, I would buy a little mileage diary at Staples and track my daily mileage, but I'm anal like that. You can then keep a basic spreadsheet of everything else (there are lots of free templates on line) and just tally things up monthly and either pay estimated taxes throughout the year or, if your earnings are minimal and you normally get a refund from your wife's withholdings anyway, you can just reconcile it all at tax time.