I like the last format proposal in the paper.
16 groups of 3, followed by eight groups of four.
After the initial group stage (two games for each team), the bottom team from each group is dropped, and the top two from each group advance into new merged groups, with results against other advancing teams carrying through. Because results carry through, each team has incentive to win on match day 3. And after that point there are eight merged groups with four teams each, so its like the current format.
Format 7: 16 groups of three, followed by eight groups of 4. The 16 groups of three are paired, e.g., Group A is paired with Group B, Group C with Group D, etc. The best two teams in each group advance to a second group stage. Teams advancing from paired groups form a group of four, and the results of the matches played during the first group stage are carried over. For example, the winner (denoted A1) and runner-up (A2) of Group A form a group of four with the winner (B1) and runner-up (B2) of Group B, and the results of the games A1–A2 and B1–B2 are carried over, so the second group stage has only four games played over two match days (for example A1–B1 and A2–B2 on Match Day 1, and A1–B2 and A2–B1 on Match Day 2. The best two teams in each group of four advance to the round of 16. Since results of the first group stage are carried over, teams have no incentive to collude. There would be 48 games during the first group stage, 32 games during the second group stage, and 16 knockout games, for a total of 96 games. The winner would play eight games, one more than in the current format and the format suggested by FIFA. Since three match days are needed for the first group stage, and two match days for the second group stage, the tournament would last at least one more week.