I agree that it's the networks that are the problem where firmwares are concerned.

When PR1.2 was released it was months before Vodafone finished "testing" their version. I'm pretty certain all bases are covered by Nokia in this respect.
People were boasting actually purchasing "unbranded" N900s with PR1.2 pre-installed and using the Vodafone network weeks before Vodafone approved the firmware. Vodafone simply used the old BS line "The Vodafone firmware is still in testing".
After more pressure they finally revealed that they hadn't even started the testing stage because they couldn't install it on their testing devices, so had to send them all to Nokia to be flashed.

With regards to Skype and other software, Vodafone have openly expressed the desire to block these at network level at least. So no surprises if they are pushing Nokia to remove them.