Oddly, I never had this problem.
I too am from the old school where buttons are on the left and the stick is on the right. Most consoles were that way, so were most arcade machines. At first, I thought having joypads with them reversed would be hard to play (just like arcade machines are hard to play when they are reversed (like DK)). But honestly, I found it easy to deal with and quite natural. So when it comes to joypads, I have no problem. But I do have a problem with stick makers now a days that insist on copying the joypad's reversed layout. Sorry, I'm right handed and simply do not have the left armed/handed dexterity needed. I can press buttons/pads with my left hand well enough, but move a stick, no. <sigh> I don't think I've seen a propper normal right handed joystick in over a decade.....
Anywho....NES. I dunno. I guess I could also say I never really loved the NES. I had a few games, like the Mario's and stuff. They were good and fun. Tho one thing that always got me was because of the tile style graphics, a LOT of the games all had a simmilar look & feel to them. It didn't seem like that many games broke out of that and used tiles in groups rather then individual units.
Even in emulation I don't play it much beyond the big games; Mario, Zelda, Dragon's Warrior, etc.. Most of the rest just seemed...mediocre.
It's funny, NES had the same problem the 2600 did; a few good games amung an ocean of crap, yet they managed to pull it off.