I would be somewhat surprised, but not totally shocked, if a certification from a DIR agency (GUE/UTD/ISE) would not be recognized, but that would likely be at a zero-to-hero dive operation, and I'd recommend avoiding those.
Since you seem pretty keen on acquiring good diving skills, why not just go the GUE/UTD/ISE route? The only issue would be if you want to go sidemount. GUE doesn't currently have a sidemount program. I have been told that it is being looked at. UTD has the z-system, and while I see the thinking behind it, I plan on going the traditional sidemount configuration. ISE doesn't have a presence in the US yet. So your choices for now are GUE and ISE. I'd recommend developing good diving skills that you will learn at both agencies (they are both excellent), and if you want to go sidemount, seek out a good instructor like Andy Davis in the Philippines or meet someone like Tom Steiner (who I plan on training with) for caves in Mexico.
It's good to know that almost everyone is aware that PADI isn't the only cert. I would be disappointed if I traveled to Fiji and they told me I couldn't dive Also, if I have a GUE cert, but want to take a PADI class with the prerequisite of having an advanced OW cert, is PADI going to let me take the class if it's GUE advanced OW cert? I assume they will but I should ask. Side mount is probably a "future" cert not immediate. I would like to find a good instructor and buy my gear from their shop, or by their recommendation. I obviously have a very good idea of what I would like, and what fits, but that doesn't mean I won't keep an open mind.