It's pretty much 100% 1 and 2.
Both the carrier and manufacturer get kickback for shipping the phones with certain apps preloaded, and since they are part of the system image, unremovable without some extra work (rooting). Every Verizon android phone, for instance, comes with Amazon Kindle/MP3, Verizon's Navigator software, CityID, and Blockbuster pre-installed, and there's nothing you can do about it.
In addition, things like usb tethering (not wifi) is supposed to be a standard feature for android as of 2.2, but is disabled in most phones.
As far as planned obsolescence, while you can't directly prove it, one nice example is Sony Ericsson, which promised for months and months that it would upgrade its X10 line to the latest android, then finally said it was impossible for "technical reasons", then announced its new line of phones, which would launch with the latest version of android.