You can install apps from outside of the Google Play store. (and open yourself up to malware) This is true, but as I mentioned before an informed person REALLY need not worry. If you are one to install everything under the sun, it may be advisable to stay away. The reason I prefer Android in this sense is because I feel the AppStore is noncompetitive. If I want to buy something for iOS, I HAVE TO go through Apple. That doesn't sit so well with me. Android essentially allows anyone, a good example being Amazon, set up shop, create sales, etc. There are often times when Google Play is an equal or better deal, but there are often times when it is not.
Apps can do anything they like in the background. This means that you can have things such as IRC clients for Android, which need to stay connected in the background. (is this something used by a lot of people?) I am not sure what you consider "a lot". To me, how many people use it is irrelevant. If it's a feature I care about I am happy to have it. If it is not, well, I could care less. 🙂
You can use live (moving) wallpapers and ones that respond to touch. (i think JB is suppose to address this a bit, but those live wall papers have slowed down the phone in a fairly noticeable way in the past) Live wallpapers work pretty nicely on current devices. Either way, this brings no utility to the device. Some people like it. For those that do, they can have it. I am the guy that could care less about this feature.
You can attach any file to and save any file from an e-mail. You can download files in the web browser. You can change the default browser you want to use. (got nothing here. i personally like safari, but i can see the value in chrome) I think this is coming in iOS6, or something like it. I don't find myself having to download files very often (ever) so I am mostly indifferent about downloads. Attaching files to email I do use on both OS's (currently using a JB tweak for iOS5.x)
You can mount your phone as a drive on the PC and copy files to/from it. You can basically use it as a thumb drive. (i don't mean this in a bad way, but if you are nerdy enough to do that then you probably have an account with Dropbox, Skydrive, Google Drive etc. These all become much more viable when you factor in the limited amount of internal storage in the flagship Android phones) Cloud storage and local storage are not the same, at least not to me. To start, not all computers necessarily have the luxury of drop box (or other cloud storage) access. In many cases it can be much quick to just drag, drop, and get on the go. You are also not having to rely on an internet connection or a cloud service, either of which can potentially go down. For important files/documents, local storage is the better choice. As far as flagship phone internal storage, simply choose the phone with removable storage, assuming that is important to you. I am fairly confident there will always be at least one flagship device with removable storage as an option. That has been Android's claim to fame for a while.
You can change the battery in most Android phones. (again....how many people really do this? I know there are some, but I don't personally know anyone out there that carries a spare battery with them) I am not sure there are numbers. I know I am the type of person that likes a spare battery on hand, but I use the phone heavily. I just like to point out that choice is always good. The person who can live without a removable battery can likely live with one (I mean just pretend it's non removable, if it makes you happy 🙂 )
You can use MicroSD cards in most Android phones. (lets look at the three "flagship" Android devices right now [One X, Galaxy Nexus, Galaxy SIII], only one of the three have MicroSD slots. seems that the trend for Android OEMs these days is to go away from offering those slots in lieu of cloud storage. meanwhile, i don't know of any android devices that come with 64GB of internal flash storage)I already touched on this a bit, but if removable storage is your thing, you will likely always have this option, or at least for a very long time. As always, it boils down to choice. If I need it, with Android, I can have it.