So my own personal contributions to this, which overlap with the OP:
1. Art. Personally, I still love the B&W line drawings and classic fantasy art. But they aren't inclusive or representative, and definitely not very welcoming to female gamers. Art that is more representative of the wide diversity of players we have today would be better.
2. Alignment. Again, I like alignment. And I think it would be great to keep objective alignment for concepts like the outer planes or some sort of metaphysical battle (whether it's the 9-point great wheel of the outer planes, or a Moorcockian Law/Chaos). But not necessary for the races and PCs if you're building from scratch.
3. Gatekeeping classes. One of the frustrating things with the way that TSR D&D was built was that they always "gatekeeped" classes and abilities behind absurd requirements; in effect, in order to get super-cool abilities, you already had to have super-cool abilities! That's why you got those ludicrous requirements for psionics, or the 17 Charisma for the Paladin, or any of the other numerous "pre-requisites."
4. Mixing granularity and genericity. This is a slightly different one, but TSR-era D&D often mixed granular and culture-specific with generic and flexible (something that still happens!). An easy example is the comparison between the Fighter (which can be easily adapted to almost anything) and its subclass of Paladin (which is an exceptionally specific type of Holy Knight).
5. Other descriptions. Sure, people discuss the harlot table. But what's worse is, for example, the description of the Goodwife that's also in the urban encounters. Here it is- "Goodwife encounters are with a single woman, often indistinguishable from any other type of female (such as a magic-user, harlot, etc.). Any offensive treatment or seeming threat will be likely to cause the woman to scream for help, accusing the offending party of any number of crimes, i.e. assault, rape, theft, or murder. 20% of goodwives know interesting gossip." In other words, this is one of the few encounters you have with a female, you can't tell the difference between her and a harlot, her only positive use is that she knows gossip, and any offensive treatment will cause her to (falsely) accuse the party of crimes such as rape. Oh boy .... There's just too much to unpack there. Suffice to say, you don't want that.
6. XP for Gold or Killing. Players respond to incentives. If the base model to advance is to kill stuff, or steal their stuff, then players are going to kill stuff, or steal their stuff. Period. If you don't want that to be the model, then you need a different standard for awarding XP (and, perhaps, kill/steal as an alternative).
7. Racial/Gender minimum and maximums.