Mess with pedals if something isn't right from a fit perspective, or like for like, you want to save a gram or two. Might not notice.
Change wheels, and you likely will notice. Faster? Not necessarily, but lots of things can make a difference to the ride (wider and lower psi smooths things way out).
A wheel upgrade is pretty easy an if anything you will only need to adjust your RD. Other things get into more work which is something to consider.
I just upgraded my cockpit to "aero" bars and love it. Not for the speed, but when I'm going really slow up hills they are wide which is great for my hands. Moral of that story, different "upgrades" mean different things with different benefits. New bar tape can make the bike seem new too.