After some research and reading others people situations I concluded that I should be filling the form as a resident alien (since the W-4 should reflect my state for end of the year)

Resident Aliens
---------------

> If you are a [resident alien][1], the rules for filing income, estate, and
> gift tax returns and paying estimated tax are generally the same
> whether you are in the United States or abroad. Your worldwide income
> is subject to U.S. income tax the same way as an U.S. citizen. You are
> a resident alien of the United States for tax purposes if you meet
> either the green card test or the substantial present test for the
> calendar year.

I pass the presence test, given the condition: 

 - 2016: 244 days since arrival 
 - 2015: 120 days in US (counts 1/3) 
 - **Total presence:** 284 which is more than 183 required

Substantial Presence Test
-------------------------

> You will be considered a United States resident for tax purposes if
> you meet the substantial presence test for the calendar year. To meet
> this test, you must be physically present in the United States (U.S.)
> on at least: 31 days during the current year, and 183 days during the
> 3-year period that includes the current year and the 2 years
> immediately before that, counting: All the days you were present in
> the current year, and 1/3 of the days you were present in the first
> year before the current year, and 1/6 of the days you were present in
> the second year before the current year.

https://www.irs.gov/Individuals/International-Taxpayers/Substantial-Presence-Test

Giving that situation, I can fill jointly with my wife, either she's being a non-resident or resident. Let's aim for the worst case, where she would not be a resident by that time, we have this alternative.

Nonresident Spouse Treated as a Resident
----------------------------------------

**Election to File Joint Return**

> If, at the end of your tax year, you are married and one spouse is a
> U.S. citizen or a resident alien and the other is a nonresident alien,
> you can choose to treat the nonresident as a U.S. resident. This
> includes situations in which one of you is a nonresident alien at the
> beginning of the tax year, but a resident alien at the end of the
> year, and the other is a nonresident alien at the end of the year.

https://www.irs.gov/Individuals/International-Taxpayers/Resident-Aliens

Other resources:

- [The Taxation for Dual Status Aliens][2]

- [Random people answering in a forum][3]


  [1]: https://www.irs.gov/Individuals/International-Taxpayers/Determining-Alien-Tax-Status
  [2]: http://blogs.hrblock.com/2016/05/10/the-taxation-of-dual-status-aliens/
  [3]: http://money.stackexchange.com/questions/49260/h1b-first-time-filing-w4?rq=1