Who actually uses the keyboard/mouse that comes in the package? I always upgrade to much better stuff anyway.
If the package comes with decent stuff, people tend to use it. I see most Mac Pros using the stock keyboard/mouse. I rarely see the more expensive Dells using them, because Dell sticks the same crap in them that they do in their cheap machines.
"Comparable" is in the eye of the beholder. If two systems both have the features that you need, they're comparable even if one has a bunch of stuff that you don't care about.
That's not really worthy of a public exercise, then. If you aren't going to compare
all aspects and features of the machine, then it's not an apt comparison, because you are prejudging the importance of particular features and producing an uneven comparison.
It's really a matter of "comparable specification" vs. "comparable value" and only the value part is subjective. In particular, the CPU can make a massive difference. If someone is satisfied with 1.86GHz cores, the 3.0GHz cores of the Mac Pro are going to be $1500+ of wasted money. But the machines wouldn't be comparable in sense that they should be fully interchangeable for any task.
The implied point you make, which is absolutely correct, is that there are other vendors offering more freedom to get exactly what you want without paying for parts you don't want. But this, quite simply, is an intrinsic feature of a mass-market system. People don't make things themselves and they don't pay for custom runs (designing a complete custom system would cost more than just dealing with the "useless" parts anyway).
How long has it taken Apple to get iTunes working on Vista? Beta 1, Beta 2, RC 1, RC 2, November corporate release, January consumer release.... And it still isn't supported!
Worked perfectly for me right through RC2. Only the RTM release killed it. The clock is still running on Microsoft getting Office to run properly on Intel Macs. iTunes works fine for the most part under Vista, they just choose not to support it.
Go to Apple for support with my Longhorn Server testing? ROTFLOL
Go to Microsoft for it or the component manufacturer. I can't think of any system components which actually rely on Apple to supply drivers on the Mac Pro (maybe the Airport card, but even that is a Netgear, I believe). They're all pretty standard, so you don't have to wait for Apple to do anything.