When we agree to fund companies, they fall into one of three buckets:
1) not incorporated at all
2) Incorporated outside Delaware and / or as an LLC
3) Incorporated in Delaware already
Those in 1) are by far the easiest to deal with - we have a standard process to get everyone set up so that going forward there won't be any problems.
Those in 2) start to get a bit more complicated and we have to work with the founders to convert to a DE C-Corp. Sometimes that means just starting anew with a new company and sometimes, if there is too much corporate history, converting the companies. This takes up some time and depending on the original state can be costly and time-consuming. But it all works out in the end...
Those in 3) are the ones that are often the hardest! There can be problems around only some of the paperwork being completed or signed, founders don't have vesting on their stock, uneven stock splits between founders (a strong indicator of future founder breakups), needlessly complicated cap tables, not enough stock authorised for us to buy our shares - the list goes on. All this can be fixed too!
The founder that says to me "we're incorporated in Delaware so you can invest in us straightaway" is usually the one that becomes one of the most complicated companies for us to invest in.
My advice would be that if you're applying to YC, then don't incorporate unless there is a specific reason to. It is much easier and cheaper for you in the long run to use our process.