I'm looking to build a Zelda: LTTP style top-down RPG. I've read a lot on the subject and am currently going back and forth on a few solutions. I'm using C#, MonoGame, and Tiled. 

For my tile maps, these are the choices I can see in front of me:

1. Store each tile as its own array. Each one having 3-4 layers, texture/animation, depth, flags, and maybe collision(depending on how I do it). I've read warning about memory issues going this route, and my biggest map will probably be 160x120 tiles. My average map however will be about 40x30. The number of tiles might cut in half if I decide to double my tile size, which is currently 16x16. This is the most appealing approach for me, as I feel like I would know how to save maps, make changes, and separate it into chunks for collision checks.
2. Store the static parts of my tile map in multiple arrays acting as the different layers. Then I would just use entities for anything that wasn't static. All of the other tile data such as collisions, depth, etc., would be stored in their own layers as well I guess? This way just seems messy to me though.

Regardless of which one I choose, I'm also unsure how to plan all of that other tile data. I could write a bunch of code that would know which integer represents what tile and it's data, but if I changed a tileset in Tiled and exported it again, all of those integers could potentially change and I'd have to adjust a whole bunch of code.

My other issue is about how I could do collision. I want to at least support angled collision that slides you around the corners of objects like LTTP does, if not more oddball shapes as well. So do I:

1. Store collision as a flag for binary collision. Could I get this to support angles?
2. Would it be fine to store collision as an integer and have each number represent a certain angle of collision?
3. Store a list of rectangles or other shapes and do collision that way?

Sorry for the large two-part(three-part?) question. I felt like these needed to be asked together as I believe each choice influences the other.