All are pretty challenging games. I'd go with Ninja Gaiden. The original Metroid is unbearable to play, IMO. --- Currently Playing: Playstation All-Stars Battle Royal (PS3), WWE '13 (360), New Super Mario Bros. 2 (3DS) "You can't sedate all the things you hate"
My only problem with getting Metroid ATM is that Super Metroid will eventually come for Wii U VC.
Metroid is still a different enough experience from Super Metroid though. If you're looking for something different then I'd recommend Super C or Ninja Gaiden then. The endgame of Ninja Gaiden should be more bearable with restore points but Super C is also a pretty fun game and is a lot less frustrating.