Okaaaay ... my own (biased) view of the changes:
#1 - The shift from TD being a small crowd of people who got really excited about the event *once a year*, to being a huge community of enthusiastic addicts whose lives are touched by TD on a daily basis.
It's been a slow, constant change, so it's hard to see - kinda like the frog in hot water - but the community right now is the biggest (and in my not-so-humble opinion) the very best part of TD's growth and change over the years.
#2 - The Token Economy.
Not just the presence of tokens (which were a hit from the beginning) but the amount of money which is spent on them, the variety of tokens (yay for trade mats & transmutes) and the whole collector's market including eBay shops and online stores. It's given a completely different flavour to the event, and to the way people interact - even in the physical space surrounding the event.
To give it some perspective: remember that Jeff once offered to dress up as Patsy if someone wanted to buy $1000(?) of tokens. The prevailing attitude was "who seriously needs that many tokens?!?"
Contrast with nowadays, where we essentially have a mini-con just to do all our Transmutes, so it doesn't take up as much time at GenCon.
#3 - The shift from One-DM-per-Party to One-DM-Per-Room.
I'll admit I kinda miss the days when your DM would follow you from room to room, because you could develop a certain rapport with them, and they could really build up the story narrative. In a sense it felt like table-top... where the DM laid out an entire world for you and your friends to share.
Now it feels a bit more like a haunted house, were you are handed off from station to station, and the narrative often gets lost.
On the plus side (and it's a significant plus!) the DMing is a lot more consistent. It was beyond frustrating if you ended up with a DM who seemed bored, or didn't know the module well, or who was slow as molasses at every. single. combat.
#4 - Coaching.
As a DM, I can not describe the difference it made to the game when Coaching and Party Cards were included as a standard component of the adventure. For the players, it may be just an extra 24 mins of paperwork, but to the DMs, it was a godsend! Can you imagine trying to run combat and keep players' bonuses in your head? Or having to ask them to show you their combat-relevant tokens at the beginning of every fight? Or springing a trap in a puzzle room and then having players dig out any of their tokens which would give them immunity to Surprise?
#5 - Party size.
Other folks have addressed the change in group dynamic, and the frustrations of larger parties. But for me, it's been (recently) mitigated by the ability to just run with fewer people.
So, in a sense, I'd consider it a big change that there are now rules in place to allow - and *support* - players' choice to run with smaller parties. It's a real game-changer for me, and the way I play TD.