Wow, I started typing this as a simple response, and it turned into more... so I'm prefacing this by saying that I don't speak for the Devs at Alla here, however, I do have an understanding of the thought and project planning process that goes on when updating to a new version of a complex website.
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Why break something that was working perfectly good in the first place.
It wasn't working "perfectly good" in the first place. The nav menu on the left had grown bloated and *way* too lengthy. Sure, it was nice to have everything a scroll and a single click away rather than a mouseover and click away, but it made the site quite messy and unprofessional looking (remember looking at a short database page and it showing a huge scrollbar because of the 3,000px long navigation menu? yeah, that's not a good thing). I would also venture to guess that the other sides of the Alla site (at least the more popular/active ones) will be undergoing a similar revamp in the very near future, WoW being first as it is the most popular MMO out there right now (by a huge margin). What better platform to test changes (and get constructive feedback) on than the one seen by the largest audience?
As far as "ease of use", like above, instead of a scroll all the way down the page and then click a link, it's mouseover a menu button and then click a link. Sure, there are a few things left out, but they're working on adding things back in and that's where we come in (see, they missed Class Trainers, the OP mentioned it and *poof* it got added.. see how this works?)
Now, of course, it is indeed different. Background colors are a bit bright for my personal taste and some stylesheet type stuff needed tweaking over the first few days (links and "user block padding" were big instances of this), but the functionality and content of the site has taken a big step forward and that's what matters in the end. Perhaps it's a bit of my controlling nature too, as the incorporation of the Wikibase (Database and Wiki hybrid) has given a lot of content control over to the users of the site. Instead of having a few content authors, there is now as many potential authors as there are users, all with the power of a very strong and very populated database of items, spells, mobs, quests, and information backing it up.
Geeze, I sound like an advertisement...
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It's not customer friendly to suddenly shift everything. More hassle than benefit. Grocery stores do it to make people hit all the aisles for sales. Exacly why was it done here?
Except that software engineers rely on different aspects of various pieces of code to ensure a fully functional (that is, error free) delivery. The different aspects of a site (I would assume that this site is much like any other, including the one I work for) rely on each other to give the user a smooth and consistent navigation through it. It may be a shock all at once, but it's either that or erroring out half the time due to different pieces being promoted at different times. (Or a hell of a lot of added developer work making their pieces work with the site under various levels of other pieces being put in place.) Simplistically, it would be like having a page that reads from 3 different files, if all 3 files are not "turned on" at the same time, the page will not load properly or be missing critical information.
Lastly, long left hand navigation bars are very 1990s (much like frame driven sites). Mouseover menus are the wave of the future! (Which, in this industry, means they'll be outdated in about 3-5... minutes).
And, as far as the old layout. I may have said the current color scheme is a bit bright for my taste... but at least it's not orange and brown!
(Just think, if my forum posts counted for entries like wiki posts... I'd be a shoe in! Book writing FTW!)