It's still mostly the same battle system, and some of the basic framework from back in 2006 (heck, some of the stuff from when the game started in 2003) has remained the same.
However, an enormous update back in mid-2007, NS-13, revamped many of the early quests and slowed down speed play in two main ways - one, by adding level requirements on consumables, and two, by adding two large new quests at levels 11 and 12, which combined are easily the length of the preceding ten; the Naughty Sorceress was moved from level 11 to 13, giving the update its name. NS-13 also added two new ascension types,
Bad Moon and Casual (no special restrictions, but the character doesn't retain a skill upon ascension, and runs of this type are ineligible for leaderboards), and a slew of other smaller changes and bug fixes.
Furthermore, they've been adding a lot of post-NS content (a clan dungeon, Hobopolis, that features some multiplayer interaction, and an optional post-level 13 underwater quest that's being steadily expanded every few weeks). This is in addition to the major overhauls they've given a few quests after it was shown - with essays and/or math, because that usually works - that they didn't work in NS-13 in their original form, relatively minor changes such as beginning combat skills for all classes and giving Moxie classes the ability to pickpocket enemies, new content from some Items of the Month in the last few years (fortunately, the items to access this content can be bought from the Mall relatively cheaply instead of requiring the donation familiars that drop the items), and a bunch of holiday content (especially Christmas, when we've gotten a nice quest and cool presents every year since I started playing again).
Oh, one more thing: Asymmetric's new programmer, CDMoyer, has done much for the game's interface in the few months he's been working for them. Things like purchasing items from the mall without scrolling through a particular store's hundreds of items or using multiple items at once from your inventory - including food and booze - is now possible thanks to him. It's also possible to do many in-game functions through the chat system, similar to many larger MMOs (especially with the macro system).