I had two separate accounts. Google merged them despite my telling them not to.

Seems to me HN covered this:

https://plus.google.com/104092656004159577193/posts/VZSLjkdq...

https://news.ycombinator.com/item?id=6745525

http://i.imgur.com/YgEjUuI.jpg

Google's proven it cannot be trusted to respect user choice, nor to not arbitrarily change the rules at a later date.

I thought I had two separate accounts for YouTube and Gmail. Not anymore. I used my Gmail address to register an account with YouTube. What prevents them in the future from buying some company, and link those accounts because I use the same credit card or some other supposedly unique identifier?

AFAIK it's required by the new terms that you give your real name. And to do much of anything you need to verify your account with an SMS to a previously unused cell phone number.

No, but google will do all it can to link them.