The most important step in any endeavour is to clearly define what it is you're trying to achieve, so it's useful to decide what this pedalboard is supposed to do. Maybe you only need a few quality-of-life pedals to get the most out of your guitars and amps. Perhaps you want to sculpt your ultimate bass tone for the studio and stage. Or it might be you're creating a living organism that is an instrument unto itself. Whatever your vision, having it clearly defined will make planning your pedalboard that much easier.
Choose pedals you use most of the time. These are what make up the basis of 'your sound'. It might be tempting to have a sprinkle of effects you only use some of the time, but every extra box on your board is going to add to the cost, weight, and complexity of your system.
A compact multi-effects unit that can change roles depending on the situation might be a better solution for adding that little bit extra without needing to devote too much space.
Think about how often you'll need to travel. A smaller, lighter board will allow you to carry it on your back, on a plane, or in the back of a taxi when the boot is full of heavier gear. If you're mostly going to be playing in a studio with just the occasional local gig, then you can go large as weight won't be as much of a consideration. Bags are lightweight, padded covers that usually include a handy shoulder strap, while cases will protect your pedals from the rigours of road, rail, and air travel.