I am considering going back to work in Canada. Last time I worked in Canada I lived in Maine. Maine recognized Canadian provincial income tax as equivalent to a US State tax. I don't believe Connecticut does this.

I will move to Canada and buy a house. My wife will stay in CT and work here. I will be paying a significant tax burden in Canada (getting the foreign tax credits but getting whacked by the AMT on the back end). Can I avoid paying CT income tax on my Canadian wages if we file a joint US Federal return and a married filing separately CT return?

Most states do not allow credits for foreign taxes. If you are not a resident of Connecticut and your spouse is, then she can file a Connecticut tax return as married filing separately.