[this long post represents my meandering thoughts - if you have a short attention span, just hit Page Down a bunch of times...]
First up, comparing yourself against Amazon "because both have lots of white" is a bit dumb. People don't go to Amazon to read stuff. It isn't like El Reg and - to be honest - thank god for the accessibility option on my iPad where pressing the button three times inverts the colours. White on black is a bit old-school, but at least I can read without eye pain.
Secondly, comparing yourself against Amazon is a bit dumb because Amazon makes good use of available screen space (their webdev mission statement probably says "a wasted area of screen is a missed sale"). You? You have huge swathes of white on either side. It looks... amateurish. Like somebody playing with <table> layouts not realising the difference between px and % because "it looks okay on my screen".
Thirdly - http://m.theregister.co.uk/Week is a 404. Any plans to fix it, or are we going to be stuck with the arbitrary order? How about give us an option - "most recent first" vs "stories we think you'd like" (or something). After all, Amazon lets you choose what order to see things in. <nudge><nudge>
Could we have an "age" indication on the mobile version, please? It is useful to see if something is "X hours old" so you can quickly scan through for items that have been posted since the last visit.
I notice that you said that you don't have in-house resources to develop, and that nobody likes change. Actually, change can be good. But to handwave concerns with "nobody likes change" is a bit churlish, especially when the change is to something that does not look or feel as nice as it was before. Here's a bit in bold, please read it twice: YOUR SITE WAS NOT BROKEN. NOW IT IS. Clear enough? Would it not have been an idea to develop this in-house, run it alongside for some feedback (maybe of your gold-shield commentators) and tweak it accordingly prior to a public release? Wouldn't that have been better than a "here's shiny new whiteness, now beta test it, oh and there's no downgrade". Reminds me of Orange with their Livebox firmware (every update looks nicer but makes simple actions tedious and breaks loads of stuff along the way - thank God they only update like once every two years).
I read the link. I find it interesting that desktop advertising brings in more revenue than mobile, given that it isn't hard to remove advertising from a desktop browser, but generally mobile devices do not have this sort of functionality. What you may actually be seeing is that advertising on a desktop machine is "tolerated" because it loads quickly (even at slow ADSL speeds) and there isn't much in the way of technical restriction. On the other hand, I completely avoid visiting advertising-heavy sites on my mobile device as it takes longer to load (an eternity if on EDGE instead of 3G), most of the browsers I have used on phones have a really annoying habit of throwing away all content and refetching it if you switch to another app (even something as simple as reading an SMS), and phone contracts tend to come with a data allowance. Some have gigabytes, some have hundreds of megabytes, some have less. I have 500MiB/month, which works out to be about 16MiB a day. Not enough to mess around with advertising I am not going to read. And, some sites, sadly, accept to receive revenue from advertisers that do really shitty things like "oh, you're on Android, here's a 400KiB apk file every bloody time" - animelyrics.com I'm naming YOU, or you visit a webpage and suddenly you are staring at some game you wouldn't look at in a million years in the app store. Behaviour like that, and the fact that bandwidth is restricted (moreso if your contract is one that will let you go over and hit you with ££££ for it) mean that people are likely to be less tolerant of advertising on a mobile platform (despite Google's best attempts to insert advertising everywhere possible). As it is, I have reprogrammed my ElReg bookmark to the mobile version as the main page is massive. I can't justify >200K every time the browser decides to reload the page. But, if it continues to be difficult to sort new stories from things that I have already noticed, I'll just stop reading it during my break at work (when I read most stuff on ElReg).
Your linked article finishes with "This is why the media industry's crumbling fortunes cannot be ignored." What was ignored for too long was the media industry publishing generic mass produced junk that alienated the readership. Take, for instance, Dr. Dobb's - a recent story here on ElReg. It started being hardcore, then it went commercial, then it went through long protracted death throes due to having lost the readership that it had in the beginning, and having lost the essence of what made it different. It might do for the publishing industry to start making things that people are willing to pay for, instead of trying to "make a killing" by publishing things that some clueless marketing twat thinks the readership might like. There's a magazine I buy from time to time. The subject matter is Japan. Things to see, interviews, lots of J-Pop, reviews of manga and such. Somewhere along the way, it started taking on a lot of stories about K-Pop. Now, I understand that maybe to a clueless Westerner, Japan and Korea are kind of the same place, but to those of us who can actually find them both on a map, they're not the same, their language isn't the same, and don't they kind of dislike each other anyway? My knowledge of Korea is a few seriously bad-ass films and That Song That Broke YouTube. Obviously, I haven't bought the last two issues, and judging by the fake sticker on the front saying "100% Japan" on the latest issue, I'm not the only one to think that. If they want to promote Korea, go for it. In a magazine all about Korea. Simple! It's really the same sort of story as Dobbs, isn't it? It's a balancing act between satisfying a potentially smaller readership versus attracting new readers while not alienating the ones they have, and not becoming so generic that their publication has nothing to make it stand out of the crowd. Perhaps, instead of whining about how mobile pays less, publishers might want to think of things that people would actually pay for...
"This may sound lame to you but we have 50 mouths to feed." - fair enough. I can't say I agree, but it's your site, your decision. You've already pretty much lost a mobile-device reader and you're in danger of making a regular become a part time lurker. Is this what you intended?