It's difficult to make secrets and multiple paths matter to the player in this format. In Port Thwomp, I use a couple secrets to hide fire flowers. I think the multiple hits allowed by the FF is a good reward for their exploration. I also make sure not to allow them to collect more than three 1UPs in the stage. When I give them one, I want it to count, so I have to be careful about how many enemies are in a line, how many coins are in the level, etc. If the level comes up at the right time in the 100 Mario Challenge, those lives have value.
Multiple paths, though? That's a really hard thing to convince somebody to go back and find, unless they're trying for an easier path after they've died a few times.
As for avoiding skipping, one must capture that elusive "just one more try" quality. Part of that is making sure that, on the next try, they can more quickly get to the point where they died. This is where both mine failed.