See, this is exactly why I'm worried. Navigation and exploration are the point of Metroid and the combat is just in there to mix things up. Because of that, splitting up the game into COMBAT MODE and TRAVEL MODE would cause a lot of problems.
Well, what I was getting at was, I don't think having a dedicated combat system necessarily takes away from anything that Metroid does well. You'll probably still be able to navigate the world as elegantly as you'd expect, only now you might have to be more deliberate about how you want to deal with the enemies in a room. Like you said, it mixes things up.
Like, let's take the Work Robots from Wrecked Ship, and imagine getting too close to them would trigger a really difficult battle. This would make the timing of your jumps around them a bit more important, or even how you pushed them around the room from a distance (imagine Ajna having a ranged weapon for this sort of purpose). You could still navigate the rooms like before, but if you were too reckless, it might take everything in your inventory to help you survive the fights.
On that note, resource and inventory management could also help encourage the exploration. Maybe some enemies wouldn't be hard to kill on their own, but since you couldn't just tank (or damage boost) your way through them, the resources needed to take them out could add up over time. That sort of tension could add a greater emphasis on learning the map, and finding alternate routes around rooms full of enemies. In these situations, you'd still be using the same navigation senses you typically use in a Metroid game, but just in a different way, with different risks involved.
So yeah, I think these sorts of ideas could actually flow very well together. I can see this game bringing us an experience that feels familiar, but still unique in a lot of ways. I'm really looking forward to seeing what L0 comes up with.
