Version: unspecified OS: Linux Depending on the number of messages the "which version to keep"-dialogue can block Kontact for hours until the user has clicked through all emails. There is no chance to abort the whole dialogue and get to work. Reproducible: Didn't try
Totally agreeing here that this dialogue creates a daily amount of irritation and the - data integrity focused - attempt at preserving data is very humble but different compared to other e-mail and PIM solutions. I would therefore opt that Akonadi gets automatic conflict resolution picking whatever option it seems best, even duplicating records with "BACKUP" in a title is usually less obtrusive then a blocking dialog in front of the user. My attempt here is to raise awareness on the fact that Akonadi is a - very beautiful - piece of tech but that it facilitates the user indirectly and not directly - e.g. Kmail has a direct relationship with the user. The less visible Akonadi and it's logo's are to the end user, the better as it gives them the "it all just works" impression.
The amount of times the dialog appears should be way less in 4.9.3/4.10. In case you see it, report how can be reproduced.