Chaewon for sure was the most unexpected winner. Yuri also was kind of unexpected (Yena/Hyewon/Minju too if i remember correctly). Chaeyeon ended up 12 when she was never outside the top 5 before. I don't think Hitomi was top 3 japanese the whole show.
Honestly i don't care as long as most of them succeed. If you make the group with the 12 highest average ranking i don't think the group has a main vocal (Eunbi probably becomes the main vocal) which is not ideal at all.
I agree that Chaewon was unexpected but let's look a little deeper
Episode 5 is when the first public votes were counted so a good place to start comparisons
So from Episodes 5 - 12 there were 5 Votes and Rankings as Episodes 6 and 7 had none so based on this
Ref: https://en.wikipedia.org/wiki/List_of_Produce_48_contestants
These contestants were ranked in the Top 12 for all 5 Votes/Ranking Episodes
Wonyoung
Sakura
Nako
Eunbi
Hitomi
So for the rest, out of those 5 Chances to get into the Top 12
Chaeyeon (4 times)
Yujin (4)
Hyewon (4)
Yuri (2)
Yena (2)
Minjoo (2)
Chaewon (1)
Those that didn't make it but were ranked in the Top since Episode 5
Lee Gaeun (3)
Miho, Miyu, Miu [AKB48] (2)
tbh, PD48 was rigged because the Japanese Contestants were ranking higher than the Korean ones so MNet banned votes from Japan