I agree. It affects people who share Apple ID's and the people who simply communicate with them. As you state about the (forced) merged thread. My experience is that it's randomly selecting the person (not just the last person who messaged you). For instance, on my phone if I'm texting John and my phone shows John, my message is actually sent to Sue. Even though the last message i received came from John, but new message was delivered to Sue.
I believe the issues are interconnected and I agree it's caused by people who share Apple ID's but the problem is still that I cannot control how people use their Apple ID's and now I cannot trust my phone when it says that I am messaging a particular person. IMO Apple has delivered a fatal blow to their iMessage App by making it unreliable. How can I know if I message someone new and they happen to share an ID with someone that my message is going to the correct person? I have no way of knowing if they share their Apple ID or not. Apple needs to respect the settings people have on their devices and not link these numbers on their servers.