Would a natural strait at Suez or Panama have the greater historical impact?
Short answerSuez, because it changes the Mediterranean itself and creates a direct Atlantic-Mediterranean-Indian Ocean route throughout history.
NotesUnlike Panama, a natural Suez opening connects a semi-enclosed sea directly to a second ocean. The deeper and wider passage would change the Mediterranean's physical circulation as well as its strategic geography. Napoleon's expedition shows one possible consequence: a fleet could continue toward India without first landing in Egypt. Distance, Indian armies, and Royal Navy control would still leave the expedition dangerously isolated and make Napoleon's return to France doubtful.