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[ChanceKJ]

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[BadMouth]

I'm picky.

I experimented with mounting depth and ended up with about 30mm between the CP top and bottom of the balltop.
I think that's somewhere between the two you show. 
On Sanwa JLF's with original shafts, that puts the mounting plate about even with the top of the CP, before a thin layer of plexi.
Any taller and I wouldn't feel like it changed direction fast enough for shmups, any shorter and I'd feel like I was moving a cabinet knob instead of a joystick.  It's still short enough to rest the palm of my hand on the CP while playing.

The type of joystick probably plays a role too.
You typically aren't inclined to rest your palm on the CP if using a joystick with a bat top and strong spring.

just my 2 cents.

[ChanceKJ]

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[RandyT]

There are a lot of factors involved in this one.  Two different sticks will feel completely different with the shafts at the same height.  The height one might prefer with one, is likely to be different with another.  The factors are centering mechanism type, throw of the stick, centering tension, switch arrangement and type, and so on.  Strong centering with a short shaft may feel terrible, while weak centering with a long shaft could feel sloppy.

Most manufacturers will tune all of this to a specific build, based on the desired result.  Unfortunately, installation requirements can require one to go with longer shafts out of necessity, even on assemblies where it may not be optimal.  In the end, it's balancing trade-offs for what the user finds most important, or replacing parts to tune the assembly to a specific shaft length.

With a longer shaft where the feel and performance is good, it's a simple matter to use spacers below the panel to achieve the desired height.  A short shaft can present a bit more of a challenge.

[ahofle]

With a longer shaft where the feel and performance is good...A short shaft can present a bit more of a challenge.

 

[yotsuya]

I'm pretty sure i'm gonna go back to the shorter sticks. but i'm not 100% convinced its whats best for other people who would play on this machine.

Do what's 100% best for you... You're the owner and the one who's going to play it most of the time. 

[ChanceKJ]

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[jaharr01]

      My wife prefers a longer shaft on her joysticks, but my shaft is short on my joystick. She also likes a bigger diameter for the shaft on the joystick, but I can't help her there either. I told her that if she didn't have such a big opening she wouldn't need a long thick shaft. Also I told her if she would use my joystick more, it may begin to feel longer and thicker to her and it would enhance her gameplay.I contacted Randy at GGG and he said they had long shafts but the diameters were all small, but he did suggest a ball top stick for her personal gaming needs.    
Jay

[jaharr01]

You know Chance most guys almost always want to go with the longer shaft.

[leapinlew]

My preference revolves around game type. Most games I could probably do either, but certain games I want a certain feel:

Defender - must use a short joystick. I was lucky enough to get a NOS defender joystick. Anything else is a compromise.
Robotron\smash TV\total carnage - definitely prefer two taller joystick balltops.
Galaga - short feels right, and I can play with a bat top, but it's just not right