I feel like every but the first 4 choices have a few problems and no real advantage (besides "looking cool" or "being different"):
Here are a few problematic scenarios:
Describing the buttons to strangers, childs, etc.
Many people don't know the name of greek symbols, chess pieces, etc. or even if they do they cannot make the connection to the correct symbol. Choices 7,8,12,15 are especially problematic since you cannot easily describe the symbols (symbols need to be common knowledge or described in three words or less. Given I probably can do that for 7: crossed out circle, melting circle, chandelier, triangle, open door and X... sounds pretty silly though).
ABXY... on the other hand are common knowledge not only to gamers, but can also be described easily to non-gamers (or at least everyone using the latin alphabet, but I assume that is covering most people and certainly more than the greek alphabet or chess symbols).
This isn't a good solution though, telling someone "Press the A button" is not nearly as effective as "Press the green button" or "Press the top button". Coloured letters help a lot (not buttons, since that would make the Pandora look like a clown car somewhat).
EDIT: To clarify: I like coloured buttons, I like the xbox controller (for example), but the Pyra does not aim to be a handheld, it aims to be a multi-functional computer and it should look like that. People using it to write mails, manage servers, listen to music, etc. might not find coloured buttons attractive and coloured labels are a good compromise here.
So you could say the lettering does not matter, but then again I don't feel like a new layout has any advantage and just alienates people.
Making a readme for your application, posting about the controls on the forum, etc.
I don't like having to look up or copy utf codes when I write a readme for my game, please keep it easy and simple
Complexity of the hardware/mould of the buttons
I assume the buttons of the Pandora are created with injection moulding and the Pyra's buttons will be the same.
Creating a mould with chess pieces or dice symbols seems much more complex than Latin or greek letters (that is a layman's assumption though, but maybe something to consider).
Licensing costs
IIRC the ABXY layout is licensed (by Nintendo?) and fees would have to be paid in order to use this - this was the reason the fairly uncommon layout of the Pandora was chosen.
I suspect the SEGA layout is licensed as well, but one would have to look into that.
Compatibility
We are in trouble here, the Pyra would like to be compatible with not only old emulated systems, but also the Pandora and possibly the GCW Zero and a bazillion other handhelds.
All of these use different layouts, so there is no way we are going to be compatible with every one of them.
Now we can try to go for the greatest common divisor, pure Pandora compatibility (to avoid work in changing ported apps again - though this should hardly be the deciding factor) or go for something completely new.
I don't know what the best approach is, but I feel like people already know the Nintendo layout or the Sega layout or the PlayStation layout and everyone has a favourite, introducing something completely new can setup an even ground, but could also alienate people and cause even more confusion...