Do you often need to press L1 & L2 at the same time? My last console was a SNES, so I'm not very aware of how extra shoulder buttons are used in games.
Honestly speaking, the PS1 is really the only area where I see this being an issue. Unless Pyra can emulate PS2, Xbox and higher, the PSX is the only system where 2 shoulder buttons is relevant, and even then, games that need them aren't in great numbers. I also guess they can be used to replicate analog stick presses as well(L3/R3).
They are way more used on current consoles, as they have been a standard for so long, and they do have minor functions, but it's nice to have more options in the palm of your hand than not enough. The beginning of dual shoulder buttons and L3/R3 is why the Wii was so successful. Gaming had become way to complex for the standard consumer, and simplicity was needed/wanted.
Now touch screens on tablets/smartphones have taken the place of what was simple on the Wii, and made gaming even more basic to the masses. I kind of skipped over the PS2 at the time, so when the PS3, 360 and Wii came around, I was like everyone else. I found the dual shoulder buttons and L3/R3 to be the straw that broke the camels back. Since I had pretty much skipped this currently, I was unprepared for the games that used EVERY button on the controller, I was overwhelmed. I was so happy to see simplicity at the time.
Nvidia has tons of cash in hand, and look at the shape of Shield Portable to see how hard it is to include everything, and still please everyone, and keep a great form. I think the Pyra's layout is very good and well thought out for what it is and does. Sadly, to keep it's Pandora esk shape, the Pyra can't fit anything anywhere. It has to work in what is there, and in that regard, as long as the shoulder buttons function when press(The Pandora could have DOA shoulder buttons), and my hand doesn't hurt after using them for 5 minutes, I'll be more than happy.
Chris