Here's some things I can remember off the top of my head:
* 2.0 used the TEXTURE1/TEXTURE2 and PNAMES lumps to define all textures. In 2.1 none of these lumps are needed; most single-patch textures can just be Doom graphic lumps between TX_START/TX_END, while all multi-patch textures (and sometimes single patch textures) are defined by the TEXTURES lump.
* This isn't a "deprecated feature" thing but 2.1 also supports tall patches unlike 2.0, which means patches/sprites can be taller than 255 pixels. This alone means we can make all skies and other large textures a single patch each, for instance.
* 2.0's barebones "SRB1 mode" typeoflevel (which just changed thok speed and jump height?) was merged with 2D mode.
* In 2.0, linedef types 405, 406, 407 and 408 all used to be linedef exec types for moving planes by linedef distances. In 2.1 we made them based on texture offsets instead, and 406/408 were removed for being redundant.
* I vaguely remember Enable/Disable 2D Mode (linedef type 432) originally being two separate linedef types in 2.0?