Ok, at first glance, I'll say this:
On the upside -
1) With regards to Hospitals etc not treating patients, this has been greatly improved even in the original now, emergency vehicles react faster and pathing is better, but I would say that the range of these building is still a little small.
2) Graphical Glitches are something I haven't encountered for quite a long time, probably about 3 patches ago. Maybe I have got lucky in that respect.
3) I've actually never had trouble getting onto a server. I'm not a big fan of the always online system, but I can't say I've ever had problems with actually logging in, once again, this may be luck.
4) Traffic congestion has been addressed by Skyways between Megatowers, which allow your citizens to travel to/from work without using the roads. It's not a perfect solution, but then that's 'sort of' the point, I'm not sure they wanted to get rid of congestion entirely. There IS, however, still a problem with people travelling to/from work in other cities until you can build railways and other public transport.
5) The exchange of utilities and cash and the co-operative building of Wonders has been patched to a much higher quality.
On the downside...
1) Still no Undo function that I can find
2) I'm still not certain the Education system is working as it should, I'll need to look a bit further into it.
3) You still get criminals and arsonists wandering in from other cities, even if that other city has no crime to speak of.
4) The water table still doesn't refill fast enough, but I think there are technologies that can be researched to improve matters.
5) It still takes forever to get rid of ground pollution from your early-game sewage works, but once again, technologies are available for this.
In summary, a lot of the main concerns raised in that article seem to have been addressed to a greater or lesser degree on the surface. I'll try to post more over the next couple of days when I can play it a bit more thoroughly.