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Manchester City, Real Madrid and Barcelona have won three out of three in the CL group stage, but they haven't qualified yet, they still need at least one more win to go through, and they prolly have to pick up at least another three points after that in order to finish in first position, which is very important to do.
You are right, but don't forget Bayern Munich who in fact have also won 3 matches so far. Bayern Munich, Real Madrid, Barcelona and Manchester City only need 1 more win to ensure they qualify for the round of 16, but two of the 4 teams mentioned will decide it today.
Manchester City play Young Boys in a moment, while Barcelona have an away game against Shakhtar in a moment. Barcelona and Manchester City have the best chances of winning, so I don't think either will fail to seal their ticket today. Barcelona has a good record against Shakhtar in the Champions League, while Manchester City looks like it needs to improve its poor record against the Swiss side in European games including the Champions League.
The other teams you mentioned above still have a lot of work to do, PSG is on six points, whilst Dortmund and Newcastle are second and third respectively in that group, and they are both on four points, it is far from over in that group.
Dortmund vs Newcastle is the most interesting match in the near future instead of Shakhtar vs Barcelona. Newcastle must win to increase their chances of qualifying for the last 16, but Dortmund, playing at home, is unlikely to lose easily. Dortmund won the away game against Newcastle, so today they will have to be good enough to repeat the same thing for any chance of qualifying for the last 16 too.
Bayern Munchen, Real Madrid, Barcelona and Man City are top of their respective groups, meaning that the four clubs can be guaranteed to qualify even though they are not group winners. The groups they are in are very balanced, two top teams and two non-seeded teams, I think the picture is as simple as that. If it's not an exaggeration, it could be said that the four clubs are guaranteed to qualify for the round of 16, whatever the scenario, they can secure one slot.
We definitely understand that Group F is a difficult group, because it is filled with clubs that have more or less the same strength, except for the depth of their squad, PSG is very dominant in this regard. It is proven that the points table does not provide room for one of the teams to become the seed, and they share the fate by having the same chance of qualifying. Maybe matchday 4 will be the decision.
Overall, the results of the 4th matchday will form a standings with a point gap, and we can clearly see the clubs that have the most potential to qualify from this group phase. It looks like there will be many surprises, because this is the round of determining fate.