I’m pretty sure you don’t owe taxes to the state where the business is registered – you owe taxes to the state in which the business operates.
Since there’s usually no liability issues in IT work, It’s just a trade off between self-employment tax, personal income tax, and corporate income tax (if there was liability involved, that may tilt the balance towards incorporation to separate corporate liability from personal liability).
Generally it depends on your state and on how much you plan to make. CA requires you to register the business in CA, so if you register in another state, you’ll have to register as a foreign corporation in CA and pay exactly the same CA taxes as a CA-registered corporation. CA has a minimum corporate state income tax of $800/yr.
Since this income will be in addition to your regular job, your personal income tax bracket is likely to be higher than your corporate income tax bracket (due to the recent tax law changes), but because of this minimum CA tax, it all depends on how much you are going to make per year – either your minimum corporate income tax or your savings from incorporation have to exceed $800/yr.
I don’t think there’s any difference in payment rates between 1099 and corp2corp – either way the payer does not pay any taxes on your behalf. There may be something about employee benefits, but contractors are not employees and don’t have all the same benefits AFAIK.
You mentioned deductions, but didn’t ask any questions about them. Business deductions have nothing to do with being self-employed vs being employed by your own corporation. In one case you deduct expenses from your 1099 income and pay taxes on the difference, in the other case you deduct expenses from revenue and pay taxes on the difference. Either way you pay no taxes on deductible expenses. Also, the concept of “standard vs itemized deduction” has nothing to do with business deductions. You should probably familiarize yourself with irs.gov.