As I am approaching completion of my build, I thought I'd document "lessons learned" to help people starting out.
Remarkably (or not) this is mostly a rehash of things posted very frequently when people ask questions or for advice.
1) Pick the games you need to play - design a control panel for those.
Well, I wanted everything, no holds barred, and my CP had to deal with that. I bought up all kinds of controls. Only later did I learn first hand why everyone says first pick the games you care about. There is no way to put all those controls together without it becoming both unusable and very ugly. Picking the games was hard, as I was not a fan of any genre. Some people light fighters, so a MK layout or 6/7 button layout is an easy choice, and the joystick is decided from a very small list. For people who want everything, fight the temptation. Try playing through a bunch of games, imagine or draw out various CP layouts, and narrow things down. Note when conceiving layouts, make room for everything under the panel - e.g. a 3" trackball is more like 6"x6" underneath (or less depending on which one you have).
Swappable/Rotating Panels: If you cannot narrow things down, swappable or rotating panels may be the answer. I didn't go this way, so cannot offer any advice or opinions. If so inclined - give it a shot.
2) Not sure? Ask.
The people on this forum are very helpful and knowledgeable - don't be afraid to ask any question at all (do a search first, it's probably been answered already; and check the wiki)
3) Cost? Erm....
If you plan well (see #6), you can manage costs well. If you go at it haphazardly like I did, some waste will occur - but I like to imagine instead that I've collected spare parts for the next build

Yes, building is addictive (this should be it's own item in this list).
4) Prototype
I went through several prototypes for CP's. Some people have done this with cardboard. I used some scrap plywood. It's easy to pop a piece of scrap under the drill and bang out button holes. You don't need much more than that to try it out. In fact, you don't even need electronics to see how it feels, what sort of elbow room you have with more than one player, etc. The caveat here, however, is that a working prototype will likely slow down progress over all. With a functioning CP connected to a computer, the urgency to build the cab is diminished. Something to be aware of. You may also use the new found time for additional planning (that's #6)
5) What's the best......?
However you end that question, the answer is: whatever works for you. Tube vs flat screen? It's a religious debate, go with whatever makes you happy or you can afford. If authenticity is the driving factor, tube it is. If you dont care, are short on cash, and happen to have a spare (anything) - it seems you have your answer. Joystick? Same thing. Buttons? Same thing. Sure, there are some products that are just better than others, but much of the debate is subjective. See also #1 above. For example, I got one of those cheapo 2 1/4" trackballs offered by Paradise Arcade and SparkFun. It doesn't spin like my 3" Betson, but that's not what I need it to do - I need it to fit in a tight space, and be cheap. It works perfectly for what it was meant to do. I have u360's, which I love, but they are pricey. If 4-way classics are your thing, get a dedicated for much less coin and a better feel (restrictor, etc).
6) Planning
I didn't do much of that. Well, I thought I was planning, but I was actually debating which spinner to get, and which this and that other thing. I should have been narrowing down which games I need to play, how to best to lay it out, drawing plans, etc. What really happened is that I ended up with various parts all over the place, forgot which bit went with what, why i got that, how that is wired, etc. Better planning and organization would have saved me a lot of time.
7) Patience
I was always too eager to get it done, and spent a lot more time fixing the damage done by that impatience. In the end, I learned to love working with wood and electronics, and that spawned several other (some unrelated) projects. And with the patience I've learned, I'm having a lot of fun in the workshop I ended up building to support the new hobbies. Having had no real experience with these things prior, patience was one of the key lessons throughout.
I had more but forget, I'll probably update this in the future. Anyone else have something to add?