The main problem with the format is that at most two teams per group can make it, but there's three slots for masters, so if the three best teams of the region are in the same group (and tbh FUT, TH and NAVI are the best three atm), one of them will definitely miss out, even if they beat every single other team.
Since Split 1+2 combined give us a full round robin, the only choice Riot made was whether Split 1 would have the intra-group or the cross-group matchups.
If they had chosen the intra-group matchups, and then made these BO1 play-in matches cross-group (2nd of Alpha vs 3rd of Omega), we wouldn't have this problem, and nothing would change about Split 2. Imo this would have been the better choice.