Currently when merging two contacts, there is no way to influence which contact becomes the "primary" one for the metacontact.
This is a problem if for example that person prefers one protocol for communication when online in both, but the contact from the other protocol is selected as primary.

This may sound like a geeky edge-case, but it's very real for example in the case of my girlfriend. She has a Google+ account, but for chatting, she only uses ICQ. However, her Google contact is still in my contact list since we of course circled each other. Therefore if she logs into Google+ and I write a message to her metacontact, it goes to her G+ even if she already closed the tab.
It's similar with Hangouts vs. Jabber: I prefer open protocols, so I want to chat with people via Jabber whenever possible, but if KTp/KPeople decides to make someone's Hangouts contact the primary one, it's actually more cumbersome (and downright impossible from the Contact List Plasmoid) to talk to that person via Jabber when he or she is online in Hangouts.

Reproducible: Always

Steps to Reproduce:
1. Merge two contacts

Actual Results:  
You cannot influence which one is the primary

Expected Results:  
You can select which contact to make the primary one.