Former New York entrepreneur here. There's a simple solution to this: don't incorporate in New York. You can incorporate in any state you want simply by having someone to receive your mail there (known as a "registered agent").
The laws in New York are absurd. I incorporate in Florida now, and it costs $70 and takes filling out a 5 minute form.
If you physically operate out of New York, that does still require paying NY State a $300/year "foreign corporation doing business in New York" fee, plus a one-time $225 filing fee: http://www.tax.ny.gov/pdf/publications/corporation/pub24.pdf
Phenomenally misleading -- a cost associated with LLCs is not a cost for "new businesses" generally; LLCs are by far not the primary vehicle for "new businesses".
LLCs are now the most popular form of business entity for new businesses. They offer the structural flexiblity and pass-through taxation of the partnership form while providing the liability protections of the corporate form. Moreover, unlike S-Corps, LLCs can have owners that are other businesses or that are foreign entities.
There are certain circumstances in which LLCs are not the best form--i.e., where certain applicable tax deductions and credits are limited to corporate entities, where VC investment is sought, or where a formal management hierarchy is required by law (i.e., for nonprofits or publicly traded companies). But generally, LLCs should now be considered the default option for any new business.
The laws in New York are absurd. I incorporate in Florida now, and it costs $70 and takes filling out a 5 minute form.