I don't think South Africa treated them as meaningless warm ups at all. I think after the Asian teams, South Africa takes ODI cricket very very seriously and a bilateral series in England right before a major ICC tournament in England is not a meaningless warm up.
That being said, the question of favourites/or not is an amusing one because you're basically making a prediction and predictions have a 50% chance of going wrong. It should not be taken any more seriously than it deserves - it's a prediction, and most analysts, journalists, and us cricket geeks will make informed predictions, usually based on past results and analysis of their performances and comparisons, but they are still a call. I think it's a bit unfair to wait for a prediction to go wrong and then come back to rub it in.
Ramiz Raja of all people was the only person who jokingly predicted an India-Pakistan final. Are we going to give him credit now for getting it right? The guy who can't even name Pakistani players? Or what if England had made it to the finals but lost to Bangladesh/India? Were we going to say then "oh see England are crap"?
Personally, I rated India and Australia as markedly superior sides to England and I picked them as favourites. I got one wrong there. But it's all about what your reasons are. We can have an informed, cricketing discussion on these reasons.
I think most people including guys like Kohli, Mark Nicholas, Jarrod Kimber who hailed England as the favourites did so based on how England bat more than what they have achieved.
So they saw a devastating batting line up with unbelievable depth, the most powerful lower middle order and they concluded England were the favourites.
For most part they were right. I don't want to be the "I told you so" guy here but the reason I rate India so highly is because despite their numbers being lower than their English counterparts since WC 2015, I just rate their batsmen as better players than English batsman (apart from Root). Ultimately, in a tournament, that makes a difference. It's hard to make a case for Australia now given what happened with their tournament, but Warner is still comfortably better than Hales/Roy combined and Smith on par with Root. But if Australia do go with the likes of Henriques at 4, then they are not going to be up there for too long
If you have a Rohit vs Hales and Hales has the higher SR and more devastating knocks currently, over a period of time, I would still pick Rohit because I am backing a more skilled player here over a player currently playing better.
England have lost to Australia, India and until very recently, South Africa too in bilateral series and that for me would place them below those two teams currently. This is not to say 'oh they are crap" and 'see how those calling them favourites have egg on their face" but just that England need to beat these top sides consistently to be recognized as a truly superior side, something those sides have done for a longer time than England.
And no, 2 years ago, Pakistan were not a better team than they are now. 2 years ago - they lost 0-3 to Bangladesh.
New Zealand - yes
Sri Lanka - same I would say. No real improvement or digression.