Well, assuming the thread title is referring specifically to what isn't in 4e, I'll have a go (but some will be repeats of things already noted). Most or all of these have appeared in the game at some earlier time.
- Henchmen, in-party hirelings, and-or cohorts
- Secondary skills and-or past professions
- Resurrection survival rolls (i.e. some chance that it does not work)
- Wild magic, chaos mages, spell surges, etc.
- Fumbles in combat
- Spells with range > "touch" requiring a roll for aiming (and that can also fumble)
- Chase rules that make sense
- Naval and aerial combat rules that make sense
- Magic items that don't make sense (e.g. a spoon that gives +1 AC (deflection) to whoever carries it)
- Non-broken polymorph self
- Polymorph other as an offensive act you don't do to your friends
- Deity-specific variants for each divine spell where it would make sense
- A quasi-logical physics for the different types of magical energy (standard, sonic, innate, etc.) and how they work. Yes, this can be done
- Standards for individual or party-based stronghold/temple/lab/guild building, development, and maintenance
- In-game real-life-based pantheons and cultures (Greek, Norse, Mayan, etc.) or guidelines for adopting same
- Guidelines for running long (10+ year) campaigns in a ruleset designed for campaigns that last less than 2 years
There's more, but this'll do for now.
Lanefan