Oooh this is a debatable question.
Short answer would be - There ain't a "best" formation.
Long answer - Depends on what you are going up against.
A lot comes down to countering the opponent's formation. But proper choices in the "Tactics" tab of the "Squad" menu are imperative to how most formations will work for your team during a live match. Furthermore, choosing a proper formation depends on what players you have in your team, and I don't just mean in terms of roles they can fulfill.
To give you my own choice in formation (and an example) - I like to play with a a 4-5V-1 the most. Works for my players, especially with the demi-gods that my AML and AMR are and the two STs I rotate around for matches. I often, if not always, beat 4-4-2s with this formation btw.
But hey, this is just my squad. Let's see what other will share as tips go!
P.S.
You don't always have to follow any strict formation btw. With enough experience with the game a Manager will start to "feel" what he/she can do in certain situations that may end up in some pretty unorthodox formations! But never forget to supplement a formation with proper "Tactics" and make sure to use the UP and DOWN arrows for players when you want your players to execute certain maneuvers during the match.