The authors example is terrible, that is an easy layout to do crossbrowser, HTML and CSS do have massive deficiencies in easily creating layouts, but so do most GUI toolkits, and compared to the other factors involved in the success of the web, fiddling around with css a little longer is a price well worth paying, for the majority at least
However, those deficiencies you mentioned are only "well worth it" because it's our only option. It's this complacent attitude that helped generate a need for a plug-in. HTML and CSS are still tedious to use and often times requires hacks to work in specific browsers. Why? We shouldn't need a mess of frameworks on top of frameworks to fix these "massive deficiencies", it's simply not good enough.
Latest Firefox, Opera, Safari, Chrome and IE10 - the bunch that supports both HTML5 and CSS3 from the start - are totally painless. That's the "HTML5 nirvana", IMHO. To be honest, breaking the compatibility between these the way the author did is quite an achievement - I really would like to see his code. Probably a quick and simple CSS Reset would solve these issues. Author's mistake is more probable though.
No upside at all? Open standards, semantic code, SEO optimization, separation of presentation and content, ability to look into the source code, ability to alter the content and/or visuals by user, better printing support, userscripts, ad blocking,... Just to mention a few.
Anyway, no matter how good Flash could have become it would always be only a plug-in. A third-party injection, not an integral part of the web - and as such it always was doomed in the long term perspective. Relaying on plugins is like - excuse an over-the-top metaphor - having nitro system in a family car. It's exciting for a while, but nowhere near an experience of having a real supercar. HTML5, in it's current state, is not yet a Ferrari but it has way bigger chance to become one than Flash (or Silverlight, or anything) ever had.
Old IE fixes a slight dirty, BUT can't get more basic HTML / CSS then this.
(Train delayed, Killing Time, Rainbows, etc.)
HTH Author.
I have no problems centering content horizontally cross browser (which he complains about).
I had a similar thought like the author recently. Flash could have been awesome with a smaller runtime, 3D sooner, progressive rendering of content (text and images getting loaded in like in the browser instead of loading bars) Who would still use HTML? There would be no upside at all, Flash has always had better tools.