s&box

A new main menu: the forest sits behind the logo with chases running across it, a slime running from the player and the player running from a boss. Six of them, covering all three bosses.
A field guide. Every enemy you meet for the first time gets a page with a portrait, stats and a line on how it fights. Boss stages get pages too, as do dodge and shield when they unlock.
Music. Seven tracks: the battle theme changes every ten waves, and each boss has a darker version of the one you're on. Tracks from OpenGameArt, CC0
Wave 30 now ends the run with a screen. Stop there or keep playing: the waves keep coming and each one is harder than the last.
You choose your first card at the start of a run.
Epics and legendaries you haven't taken yet come up more often, until you've collected them all.
How cards work is explained on the first upgrade screen.
Death animations for all three small slimes.
New decor: a tree, a fallen log, rocks, bushes and six mushrooms. Scattered without overlapping, and you walk behind them. (Thanks SakuSato)

Enemies you can't see can't be shot. Auto-aim used to reach anywhere on the map, so the safest way to play was to run and never look back. Weapons now only fire at what's on screen.
Weapons fire on their own, no holding the button.
Dodge unlocks at the first boss and shield when ranged slimes start appearing, instead of being handed to you in the first second.
One upgrade card per ability instead of four. The pool is 25 cards instead of 33, and each is worth more.
Enemies arrive from around you rather than from anywhere on the map, and start closer during the first five waves.
Pause, death and guide screens animate in, and buttons respond to hover and clicks.
Upgrade cards fly in, and the one you choose flashes before it takes effect.

Endless mode past wave 30 was rock slimes and nothing else, because wave 30 is a rock-slime boss wave. It now mixes all six enemy types.
Bosses dealt the same damage on every boss wave, however far into the run you were.
Bosses stopped summoning when the field was crowded: ordinary enemies counted against their summon limit.
The mid rock slime could never reach you with its melee attack.