Just to scratch the surface:
The entire Mach kernel architecture as used by Apple is ineffective due to its massive communication overhead and synchronization issues -- this is what causes the annoying beach ball to appear.
Monolithic kernels, as for example Linux, suffer from other issues that can affect stability, but they generally provide MUCH better performance. It actually is no wonder or miracle that Linux runs circles around Mac OS X on the SAME Mac.
You could fill books with what Apple could and should have done differently. It's not just limited to the lower system parts like the kernel. Their esoteric choice of programming languages that NOBODY else in the ENTIRE industry uses is another example for their rather obscure design selections. Then there is the Dock that is one of the poorest GUI decisions they ever made - even Microsoft's Windows 95 Start Menu was already years ahead of this (hierarchical program groups are simply a MUST HAVE when you have more than a dozen applications installed on your system).
And just let's not forget Apple's ridiculous design choices when you try to copy a folder to one with the same name - they DELETE(!) the existing target folder instead of doing what EVERYBODY else in the industry does: MERGE the content.
But it goes along with Apple's abuse of the word synchronization: They simply delete the target and put the content of the source to the target. Well, my friends, just let's be very clear here: Synchronization, in the true meaning of the word, which is "COMBINE", is a BI-DIRECTIONAL process.
Apple might provide a user-experience that is more comfortable or better than what most of their competitors provide, but they are FAR from being perfect.