New Formats Post 2024-

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Awarding EPS after rebalancing might create some very weird situations. If Czechia had finished at top2 of the season ranking and leagues had finished as it is now then Sparta would have taken the CH spot and Slavia the N2 spot. Since rebalancing is done before awarding EPS Sparta takes part at the rebalancing contest for CL-W and EL-W but due to low coefficient remains at Q2ch while Slavia is promoted from Q2nc to Q3nc since Benfica wins the EL-W rebalancing and Slavia has the highest coefficient from the clubs of Q2nc and replaces Benfica to Q3nc. Then EPS should be awarded and Sparta as champion moves to LP, Slavia replaces Sparta at Q2ch and Plzen replaces Slavia at Q3nc. The outcome is Slavia that had a secured spot at EL-LP might not qualify even at ECL-LP

Awarding EPS slots after moving the champion with the highest coefficient to league stage may make sense at the instance of Slavia winning the championship and has the highest coefficient in the Champions path then Sparta Prague can also start in the league phase through EPS.

Edit: The same applies to Portugal: Benfica 1st, Porto 2nd EL TH spot, Sporting 3rd EPS spot.

But It's weird anyway that a champion can start in Q2 and the runner up in Q3 of the same competition.
But you have since 2015 3rd placed teams of associations 10-12 (6-9 as well in 2015-18) guaranteed EL/ECL groups while runners-up may get completely out when CW qualifies for UCL. I didn't see any team trying to finish third instead of second in their leagues.
The same would apply for Slavia Prague who has bigger chances for CL groups starting in Q2ch then Q3nc.

Finally the changes in coefficient calculation with the bigger increase in CL points in relation to EL and CoL (and in EL to COL) should make it even harder for an 11-55 NA to make it to top 2. This may have been the last season with actual chances.

The Portugal example is different. Assuming Portugal had finished at top2 with current standings Sporting as CH will qualify to CL-LP, Benfica as N2 will qualify to CL-q3nc but since they have the highest coefficient will move to CL-LP if EL-W qualifies to LP and N3 Porto will use the EPS and take part at CL-LP since there is no club from Portugal at qualifiers. If Benfica overtakes Sporting in league then Benfica will take part at CL-LP as CH, Sporting will be at CL-Q3nc and will remain since hasn't big enough coefficient to win the rebalancing spot but due to EPS will move to CL-LP and Porto will replace Sporting at CL-Q3nc. If EPS spots were awarded before rebalancing Porto would move to CL-LP in both cases because they have same coefficient with Benfica. My point is that we have different outcomes for a club without depending on the club.

Also in a more realistic scenario that can happen Germany finishes at top2, and Dortmund wins CL and finishes 5th. The 4 German spots to CL get direct entrance to CL-LP, Dortmend as CL-W also qualifies to CL-LP and since rebalancing is done before awarding EPS it is not needed. Then awarding the EPS to Dortmund is impossible since they are already at CL-LP so we have an extra spot free. Will there be rebalancing again based on coefficients or is it at the category 3.06 or will the board decide? The same issue exists if EL-W finishes 5th in domestic league eg Roma or Atalanta