As always, there are some problems IndexedDB document stores solve well, and others that SQL is really well suited for, and I think it's great to have both options. What sucks is when people say "Sure, we'll support that there is more than one way to do this (TMTOWTDI), as long as you recognize that my way is the right way in almost all foreseeable cases, so we'll build the tool this way". That statement is rarely correct, especially when making a browser capability. (Yes, I know, trying to disprove a generalization with a generalization isn't very persuasive. Oh well.)
I read all the concerns (it's a standard built around sqllite, and who wants that?!?!, etc.) and I still sigh a sigh of disappointment that it's come to this. I know, Web SQL isn't going away, as the author points out, but it will be a 2nd class citizen for the foreseeable future, and that's just a missed opportunity, imho.