1. An actual final boss, since before 1.3 all we had were Skeletron Prime (kind of) in 1.1, the Golem in early 1.2, and Duke Fishron in late 1.2. None of them really felt enough like a final boss.
2. For the SDMG to actually be added in. Seriously, you have no idea how long I was looking around for a way to get that thing as soon as I found out about its existence. Then I found out it wasn't available when it was originally added.
3. Better stuff from fishing. Most of the pre-1.3 fishing loot didn't really feel like it was worth the time, but now we get really useful items and good weapons from fishing instead of just ores and better fishing equipment.