This last minute change is so dumb I am finding it very hard to believe Apple actually did it.
In the first place, there was nothing "wrong" with the perspective of the dock on the side because there is no accurate or sensible 3D perspective in the entire system. It's primarily isometric. At the very least, the perspective dock on the side has exactly the same amount of 3-D "realism" as it does on the bottom. If one argues that it's wrong on the side, one must also argue that it's wrong on the bottom. The entire GUi is "wrong" in this way in that light. There are no "lights" that create the drop shadows, no "proper" perspective anywhere, and as others pointed out previously, by the same logic all the icons should fall into a pile at the bottom of your screen.
In it's own way, this paragraph is like the 3d side dock: lacking internal logic, self-contradictory, confused. "One" doesn't have to argue it's wrong on the bottom if it's wrong on the side - they're two different perspectives. The bottom is a shelf with icons poised sturdily on top of it, waiting for you to caress them with your mousey and spring to life. By comparison, the 3d side docks lost all meaningful perspective in the translation. Instead of icons sitting on a bottom shelf, the side shelf became a window flap pushed open, with mysteriously floating icons severed from any direct relationship with the flap that so valiantly supported them on the bottom. Untethered and scatter-brained, the side icons threaten to collapse into a big oogy mess and spill sebaceous bromides all over your keyboard. The icons on the 3d bottom, however, are supported, confident, and ready to do battle.
Secondly, all this has done is introduce an interface inconsistency. That's just plain stupid.
Yes, now it's inconsistent. However, they obviously debated the pros and cons and decided that maintaining consistency at the expense of a nonsensical assault on the third dimension wasn't worth it. The choice was between consistency for its own sake vs. a more elegant and sensible design that doesn't make their users get nauseous, throw up, and create 400 post threads on the interwebs complaining about it.
The only way around it is to let people choose between the two looks regardless of where their dock is.
No, there are many ways around it.
A good designer designs something based on strong heuristics or design principles, not on how many people whine the loudest about what.
No, a good designer designs good stuff rather than quotes pompous rules from a design 101 text book. Furthermore, there's no evidence that whining had anything to do with this change, although if it did, so much the better.
Anyone who has actually designed something can tell you that it has nothing to do with just taking a list of "wants" from the users and trying to implement as many as possible. We all know there are going to be a dozen shareware dock modifiers a week after Leopard is out anyway. Apple should have let those people define the "alternative" dock looks IMO.
What makes you think this is still not the case? Apple is only offering what they believe is the best current design by default. You're still free to tart it up to your heart's content. Incidentally, I believe this 11th hour change is a stopgap measure until Apple can implement a 3d side dock that is elegant rather than flawed. However, the 2d stopgap is better than the 3d fiasco.
Finally, when you start to cave into whiners and complainers you open up a Pandora's box of trouble as can be seen on this very thread. Not two seconds after it's done, you already have people wanting even more. Already there are posts whining about how they want the same look on the bottom, and what about those like myself (and others on this thread), that actually like the dock on the side and want the 3-D effect?
Most of the posts are praising a decision that reflects early user feedback. On the other hand, you are whining like a big fat whinoceros, and in that I agree that it's a Pandora's box to cave into your sort of whining.
If it turns out that this is just an option for either the side or the top, then IMO it's a bit shameful of Apple to do it, but understandable. If however, as this article suggest, this look is only for the dock when it is on the side and cannot be changed, then it's the lamest, dumbest GUI decision I have heard of in a long time.
Then it is a good thing you likely do not have much experience with GUIs. The number of truly lame, dumb GUI decisions on competing products might be too much for your constitution to withstand, given your reaction to this relatively trivial but otherwise sensible revision.