In addition to the formation, updating player morale and condition is a wise idea. How much you want to update them is up to you, since resources are limited. From my experience, I've lost matches when countering the opponents formation, when I didn't fully update player morale and condition. For example, I just lost the 2nd leg of CL semi-final 1:0 while using 3n-1-4-2 against a 4-1-2-1-2 while having the stronger team.

Also if using 3n-1-4-2 against a 4-3w-1-2, be careful of his wingers. If they aren't quality players or in poor form, you should be ok, but if they're quality and/or in-form having no flank defense could prove costly.