One of my friend (Indian) in H1 came to US in Oct 2005 and his wife came to US in Feb 2006. He did not meet substantial presence test and he will file for extn. And then file 1040 after meeting the presence test.

1. Whether he can file for Married Filling Jointly even though his wife was not is US during 2005.

In my opinion, yes he can. There is no residency requirement explicitly stated in either IRS Pub 17 or IRS Pub 519.