@WHEREAMI what is your biggest concern? it's not clear.
as long as you and your spouse are willing to file a Joint return, even if you are separated, there is no issue.
the issues surface is one or the other is unwilling to sign the Joint return.
Don't over look the lost Tax benefits of filing Separate - you lose any educational tax benefits.
Filing Separate ALMOST NEVER makes sense financially (96% of married couples file Joint(. (It may make sense emotionally - e.g. both are unwilling to sign a Joint return)
