1. "Natural scrolling" When you scroll down on a laptop, you expect the page to scroll down, not up.
Bald's question was what features were added that were bad for a desktop OS. Adding the option to change the scrolling is not bad. If you don't like the new way, use the old one. I prefer the new one. I expect, on my laptop, for my scrolling to behave as it does on my iOS devices. But again, since it is optional, this isn't bad for the desktop OS, it is only good.
2. Gigantic Safari tabs. Displaywide tabs might have been good for a 7" wide screen but for a 12" wide screen, it's just a horrible implementation of tabs.
Haven't seen them so can't comment.
3. Notification center's implementation. Like I said, Growl's implementation is much better, with an overlay instead of a screen push-away.
So because you prefer the way growl does things, it is bad for the desktop OS to have notification center? Are you even be serious at this point? If you prefer growl, use growl. Those who prefer notification center will use it. Again, adding options and diversity is good, so this is a non-issue.
4. Launchpad. Dumbest idea ever especially when we have the Applications folder and/or Quicksilver.
Launchpad is purely optional, again. So this isn't bad for the desktop OS environment. It seems you don't know how to comply with a simple request as this has already happened multiple times now. If you were ever a student, I hope you didn't ignore specific instructions as badly as you do here. And if you work for a boss, I hope you don't just ignore what he wants and do your own thing. Be sensitive to what is being asked of you.
5. Dumbing down of utilities like Airport Utility. Seriously? I have to download a legacy version of Airport Utility to change certain basic settings on my Time Capsule, but can't use iCloud with it?
Legacy version? 5.6 was released the same day as 6.0. 5.6 does some things 6.0 can't, and the only thing 6.0 does that 5.6 doesn't is it allows you to enable back to my mac. Additionally, 6.0 is likely incomplete right now, just as Quicktime X is incomplete. Expect future versions to re-incorporate the features of 5.6 Apple is well aware of its limitations, that's why it rolled out 5.6, and will continue to support that old paradigm, until the new one is ready to fully replace it. I know it is inconvenient to have to use two utilities, but since back to my mac was broken in 5.x series in iCloud, I'm glad Apple chose to release 6.0 incomplete than have us wait until all the new features are in it. Good temporary compromise on Apple's part.
6. Mac App Store. iOS doesn't have firmware updates provided through its App Store; why should Macs do so?
Rather than software update you now use the MAS. Everything happens in one place and with a much nicer graphical interface. This is good news so I don't know what you are complaining about.
Why should developers have to give 30% of their profit to Apple just so they can implement iCloud and Notification Center? It's not like the Mac App Store popularizes new apps like App Store does. Sooner or later a hacker is going to crack Notification Center so that it can be used by any app but the current rules are just too ridiculous. (Although the app discovery portion of MAS is somewhat neat)
Because they are using Apple bandwidth and storage space. What are they suppose to get it for free? Also, keeping iCloud APIs restricted to MAS is likely to keep the Cloud safer. Everything in the MAS is sandboxed where you don't have access to other applications within your own application (yes I'd like to see that change from sandboxing files to app, from apps to files types, but regardless). Nothing is stopping you or third-parties from writing your own Cloud type APIs and using those to distribute your Cloud based features. I'm rather surprised to hear someone complain that iCloud is bad for the desktop OS environment. Seriously. Some people just like to complain I guess. You might not like iCloud and how Apple rolled it out, but I think it is a very good thing to have. But here is the important point for you to remember, since you just don't seem to get it. iCloud is purely optional so it can't in principle make the desktop environment "bad" or "worse". Ignore it if you don't like it.
Also, if a hacker does get in and expect to use the APIs, expect them to get promptly sued. There is a reason why Siri, though cracked, isn't being widely used.
7. Loss of physical media. I'm gonna get flamed on this one. Software suites like iWork and iLife will soon be exclusively digital, as Mountain Lion is also (although you can burn the ESD DMG to a USB like Lion). What if your internet is throttled and/or have slow internet? Monthly caps? Not all of us have fast internet with unlimited usage, and for those of us who use satellite internet or DSL, if internet is down, physical media would be very useful.
That isn't Apple's problem. Complain to your ISP. Apple's digital delivery is cutting down costs and more environmentally friendly. This is a good move.
8. Notes and Stickies as separate applications. Redundant, don't you think?
Sure but you can get rid of, or ignore, whichever you want. How is that bad for the desktop OS environment? You really struggle with that concept huh?
9. Messages wasting so much space, and the inability to see the full friends list in fullscreen mode.
Don't use it then. It's optional.
10. Game Center. Steam and Origin really will drive this new app to oblivion.
Sigh. Is it even worth repeating at this point?
11. New skins. Does iCal / Calendar really have to look like a paper calendar with a faux leather binding? Isn't a simple unified interface a much better option, not to mention more eye pleasing?
Nope.
12. Gatekeeper. I'm sure there's been extensive debates about this so I won't even explain this one.
Nice. You realise this is so controversial, rather than actually say more to make it somewhat plausible, you resort to saying nothing. Why did you even include this in your list. Trying to stretch things are we?