I have both and feel they're pretty much on par with each other. Ninja have slightly note flexible combos while Samurai are at the mercy of their Sen, especially if they don't have Hagakure to clear it. Ninja are more complex teamwork wise because they want to try and match Trick Attack with other party buffs for maximum gain while Samurai can pretty much focus on what they're doing. They both have a couple positionals. Almost all of the Samurais OGCD abilities require Sen management while Ninja are basically just use on cool down except for the newer abilities that use Ninki. Samurai have to manage their resource more than Ninja, but Ninja have mudras.

Overall, neither one is as difficult as say, DRG or MCH, but both require some skill for maximum potential. So, go with whatever class you think you'll have more fun with as I feel both are fairly equal difficulty wise.