Before you choose your ideal counter formation, you need to compare both teams quality in order to decide about your team's orders.
Team Mentality
If you are better 1 star or more quality, choose attacking mentality. If your opponent is better choose defensive mentality.
Focus Passing
If your formation has wingers focus passing should be set on down both flanks. If your formation has AMC focus passing should be set on through the middle.
Pressing Style
Own half will do for 95% of your games. Whole pitch is only suggested when your opponent is really weak and you need to dominate the match.
Tackling Style
Normal for any team with a small roster to avoid injuries/cards. Hard for every team with a full roster that can take the suffering throughout whole season. Dont even try easy option.
Passing Style
Short will provide passes only if your lines are close to each other.(for example AML+AMR between middlefielders and strikers). If you are not sure about it, it is recommended to go with mixed. Long blends well with defensive mentality and counter attacks checked.
On a side note: short passing will boost your passes completed % ingame stat, while long passing will make your attacks occur faster.
Marking Style
Always play zonal because this way your players cover each other.
Force Counterattacks: Only with defensive mentality and long passes as mentioned above.
Play offside trap: Only if you have compared both teams speed and you are faster. Three defenders perform offside trap much better than four.
The following are only suggestions, they are not game changers.
Let's not forget there is a thing called RNG (Random Number Generator) and sometimes can mess things up pretty bad, no matter how awesome you are as a Football Manager.
Opponent's Formation
5-4-1
5-3N-2
5-3W-2
5-1-3N-1
5-1-3W-1
5-1-2-1-1 Narrow Diamond
5-1-2-1-1 Wide Diamond
5-2MC-(2AML/AMR)-1
5-2ML/MR-2AMC-1
5-2MC-2AMC-1
5-2-1-2 X-Style
5-1-1-1-2
4-5-1 Flat
4-5-1 V-Style
4-4-2 Classic
4-1-2-1-2 Narrow Diamond
4-1-2-1-2 Wide Diamond
4-1-2MC-2AMC-1 Loop
4-1-1-2W-2
4-1-1-2N-2
4-2DMC-1-2AMC-1
4-2DMC-1-2(AML/AMR)-1
4-3W-3
4-3N-3
4-1-3N-2
4-1-3N-1-1
4-1-3W-2
4-1-3W-1-1
4-2DMC-3W-1
4-2MC-3N(AM)-1
4-2MC-3W(AM)-1
4-3N-1-2
4-3W-1-2
4-3W-2AMC-1 Xmas Tree
4-3N-2AMC-1
4-3N-2W-1
4-2-2-2 Hexagon
4-1DMC-2MC-3
4-1MC-2AMC-3
4-2-1-3
4-1-4-1
4-4-1-1
3N-5-2 Flat
3W-5-2 Flat
3N-5-1-1
3W-5-1-1
3W-4-3
3N-4-3
3W-1-4-2
3N-1-4-2
3N-5-2 V-Style
3W-5-2 V-Style
3W-2DMC-3W(ML-MC-MR)-2
3N-2MC-3W(AML-AMC-AMR)-2
3W-2MC-3W(AML-AMC-AMR)-2
3N-3MC-2W(AML/AMR)-2
3W-2-3W-1-1 Maple Leaf
3W-1-3W-2(AMC)-1
3N-1-3W-2(AMC)-1
3W-1-3W-1-2
3N-1-3W-1-2 Dandelion
3W-1-3N-1-2
3N-4-1-2
3W-4-1-2
3N-2DML/DMR-3N-2
3-2-2-2-1 Butterfly
Counter Formation
4-4-2 Classic OR 3-5-2 Flat
3N-4-1-2 OR 4-4-2 Classic
3N-4-1-2 OR 4-4-2 Classic
3N-5-2 V-Style
3N-5-2 V-Style
3N-5-2 V-Style
3N-5-2 V-Style
4-4-2 Classic
4-2-2-2 Hexagon
3N-1-3W-1-2 OR 3N-1-3W-3
3N-1-4-2
4-3-3 OR 4-2-2-2 Hexagon
3-5-2 Flat OR 3-5-2 V-Style
4-5-1 Flat OR 3N-2W-3N-2 OR 4-3N-3
3N-4-1-2 OR 4-5-1 V-Style OR 3-2-2-2-1 Butterfly
3N-5-2 V-Style
3-5-2 Flat
4-2DMC-2MC-2 Hexagon
3N-3W-2MC-2
4-5-1 V-Style
3N-1-4-1-1
5-2MC-2(AML/AMR)-1 OR 4-4-2 Classic
4-4-2 Classic OR 4-5-1 V-Style
4-1-4-1
4-3N-2(AML/AMR)-1
3N-5-2 V-Style
4-5-1 V-Style OR 4-4-2 Classic
5-1(DMC)-2-2
3-2-2-2-1 Butterfly
3W-2DMC-3W-1-1 OR 3W-2DMC-3W-2 OR 4-4-2 Classic
4-4-2 Classic
4-3N-2(AML/AMR)-1 OR 4-5-1 V-Style OR 3N-5-2 flat
4-1-4-1 OR 4-5-1 V-Style
3W-2DMC-3N-1-1 Eiffel Tower OR 4-5-1 Flat
3W-2DMC-3W-1-1 Maple Leaf
4-4-1-1
3N-4-1-2 OR 4-4-2 Classic OR 4-5-1 V-Style OR 3-4-3
4-1-4-1
5-1-3W-1
4-5-1 V-Style OR 4-3N-2W-1
4-2-2-2 Hexagon OR 3W-4-3
3-5-2 Flat OR 4-5-1 V-Style OR 3W-2N-3W-1-1
3-2-2-2-1 Butterfly OR 4-3-2(AML/AMR)-1
4-5-1 V-Style
4-1-2-1-2 Narrow Diamond
4-1-2-1-2 Narrow Diamond
4-2-2-2 Hexagon
4-3N-2(AML/AMR)-1 OR 4-4-2 OR 3-5-2 OR 3-2-2-2-1 Butterfly
4-1-2-1-2 Narrow Diamond
4-5-1 V-Style
4-3N-2(AML/AMR)-1 OR 4-2-2-2 Hexagon
3-2-2-2-1 Butterfly
3W-5-2 flat
4-4-2 Classic OR 4-5-1 V-Style
4-4-2 Classic OR 4-3-3
4-3N-2W-1
4-5-1 V-Style
4-5-1 V-Style
4-5-1 V-Style
3-2DMC-3-1-1 Eiffel Tower OR 3N-5-2 Flat
4-5-1 V-Style OR 4-4-2 Classic OR 4-1-2-1-2 Wide Diamond
4-5-1 V-Style
4-1-2-1-2 Narrow Diamond
4-1-2-1-2 Narrow Diamond
4-4-2 Classic OR 4-1-2-1-2 Narrow Diamond
4-2-2-2
"W" = Wide
"N" = Narrow
"V-Style", "Narrow Diamond", "Wide Diamond" etc. = How the formation looks on the field.
Use at your own risk. If you have to choose one formation out of two or more, pick the one your players are better than your opponent's and on good shape at that given time.