For the consumer, it's better to have an OGL only game. Because in the case of a setting or rulebook, you don't also need the D&D PHB. And they don't have to follow the new d20 content restrictions.
For the company/seller, it's better to have the d20 logo, for advertising reasons.
This also applies to the consumer, somewhat, because say you see a new supplement in stores on a subject you really like. If you're a d20 fan, and you see the d20 logo, you'll probably definitely get it, as you know it's for a system of your choice.
But if it's OGL only, it can't have a d20 logo, nor can it mention D&D (because of one of the clauses in the OGL, you can't use trademarks of another company for compability purposes, which is normally legal, like for generic drugs and such). So companies have to use euphemisms, like "Compatible with the 3rd edition of the world's most popular role-playing game"
This is very tricky for small companies. If you see the Quintessential Monkey, you know it's probably know it's a Monkey splatbook for d20 from Mongoose, just by the title. But a smaller or newer company doesn't have that same name recognition built up.