There are far more software project starts than good names out there.

I doubt that. Define 'good name'. Also, for open source software it does not matter that much what it is named. Who would care if Python was named e.g. Snake or Juice or Foo? As long as it is somewhat unique and catchy it should be fine, shouldn't it?

  You don't know which category your project will end up in when you start it.

Exactly, you do not know it. If your product is successful you want it to be unique. Just imagine the number of wrong tags on SE. And if you product is not successful it is even worse to add unnecessary confusion.

  Because JS is popular

Surprisingly and unfortunately, yes. But other technologies have had their time as well, e.g. I can't remember any ambiguous naming in Java. Anyone?

  There are also a lot of half-baked libraries out there that will waste your time. So many developers end up making their own.

Ok, why not just name it jQuery then? Hardly an excuse for poor naming choice.