This can be a hard one to answer.  So much depends on the space you have and of course money available.  

One thing I can offer is that don't "hide" your supplies!  I really like tubs for storing things like fabrics but if you don't label them you'll never take the time to look in them when you need a fabric... trust me.  Invest in a label machine.

The shelving you can get at most home stores is not too expensive.  You can get the cheap brackets to hang them or the more expensive track bracket system. The track system is more versatile since you can move the shelves up and down easily. This along with small clear tubs (gotta see the stuff inside) workers well.

I like to have my brushes and sculpting tools handy.  Keep them on the table in your third and fourth favorite coffee mug. I use my favorite and second favorite for the coffee.  For some reason, I seem to end up with a lot of souvenir coffee mugs. 

I think you have a good point about not  hiding or clear bins to see things quicker but seeing all that detail is stressing to my husband, he thinks about how much money I have spent on all those things. Cas said a good compromise was frosted plastic with large labels. I like the Cricket Joy label maker cutter and printer to make some pleasing large labels. One thing that Cas said that was new to me was to store things according to how often I use them.  One crafter she gave entire wall of pegboard but painted it a pretty color instead of the ugly brown like in our garage. That could be flexible as your needs change and keep often used tools handy without using much space. I want to spend more time creating than looking for fabric or tools. 

Organization? I don't believe I am familiar with that word. I used to be organized actually but then we downsized and moved to a smaller house that left me with less room. No matter what your space, the number one rule of thumb has to be to have a specific spot for everything and, when not being used, it goes back to its spot. If not, things start to migrate out and find themselves being misplaced, a lot, then you find yourself being one of those people looking all over the house for your fabric pencil that has been stuck behind your ear all afternoon...don't ask, it was a missed caffeine day. 

Yes those fabric pencils are tricky little things. I search for long time to find them and then they are expired. I think I will just store those tricky devils at the store, I can always find them there. Someone needs to make a better quality fabric pencil.

My son gave me a Cricut Joy for birthday and it is so much fun, but funny thing is I have now gone off on a bunny trail of other paper crafts that need other supplies....so less organizing going on but more fun. If I had one of these cutting machines years ago I could have done so many things faster, they are amazing. As I age and cutting tiny things like eye pupils gets harder I can rely on this cutter to cut for me with perfection. After two month of the little Cricut Joy I got a bigger Explore model on Black Friday for half price. This is addictive!