I've been taking mtx for quite a while now, and I still have mild nausea and fatigue a few days after taking my weekly dose. I take 15mg/week. I've noticed that some weeks are much better than others, though, with respect to the nausea. On a good week, I simply won't have an appetite. Occassionally, the day after I take it I'm severely nauseated, but can manage light food and plenty of fluid. The nausea and fatigue, I'm hoping, will disappear in time. I've been taking mtx for a little over a year now.
Mtx has made a world of difference for me as well. I hope it does for you too.
Current dx: Rheumatoid Arthritis