Madotsuki said:
Focus on the level design, then add cutscenes and details later? Just do the cutscenes in order?
Generally speaking, those two approaches are called top-down and bottom-up.
Making something top-down essentially means making a large, vague plan, and then working the smaller details out as you continue.
Working bottom-up means that you start with the small things, and they build together to make something larger and more complex.
Top-Down:
+ You can better control the flow and have a more sweeping story
+ In metroidvanias, the different zones tie together better and make more sense
- Often it is hard to follow a more general outline while you are actually modding
- If you don't have a good foundation, it is very easy to plan beyond your abilities.
Bottom-Up:
+ Smaller details interact better
+ Much easier to finish
- Gameplay is generally more linear
- Anything you add as an afterthought will seem very out of place
Of course there are others, but those are perhaps main pros and cons. You should decide yourself which way to go, but for a beginner I'd surely recommend bottom-up. Even for the more advanced modders, I'd say a combination is better (I almost always work top-down, and I have nothing to show for it).