This quickly became a sore point for me. On the one hand, there's nothing stopping the characters (players) from trying to take a short rest after every encounter. Throwing additional encounters (wandering monsters, etc.) can often ruin the story and flow (just like excessive rests) and over time feels punitive.
While I understand the purpose for tying certain abilities to resting, it also had the affect of impacting the story-telling. So I decided that ultimately the questions I wanted answered were:
How many times did I want the PCs to be able to use their 'short rest' class features?
How often did I want them to be able to heal?
What activities or actions were needed to accomplish these, and how much time was needed?
Ultimately - do they need to be tied to a story element (like stopping to rest) or can they be addressed differently?
As always, for a published game, they've got to come up with something that works for 'everybody' so my rules may work better for some than others. But here's what I've come up with.
Healing - Hit points are abstract representing many things in D&D. I've added additional healing for healing kits, healing classes and the healing feat give a bonus. In addition you have your 1/2 hit dice to use when you want. Outside of combat, I assume that unless circumstances dictate otherwise, you're taking 10-15 minutes to catch your breath, tend your wounds, etc. and that's plenty of time to recover hit points. So this takes a little time, but doesn't have to be tied to a rest.
Class Features - Many of these require some actual time as well as energy to recover. Studying spells, praying, meditating, etc. These are better suited to something that does take time, and centered around traditional breaks for meals, etc. is a good option. Replenishing mind and body with food, water, study and rest. I've set these at 30 minutes minimum, maybe an hour. In general I think the idea of recovering these abilities twice in a day is reasonable. This is as arbitrary as any other ruling, mind you. But it also kind of makes sense, perhaps for certain abilities more than others, but it's good enough for me.
Long Rests (sleep for the night), is pretty much as written.
Monsters have a recharge for their special abilities. If they manage to escape multiple times they can recharge their special abilities over and over, where you can only do so as many times as you can take a short rest. The rules don't limit these directly, but tie it to the ability to take a rest. I'm OK with them recovering them multiple times during the day, but so far have capped it to twice. So a 2nd level druid can shape change 6 times a day (for a maximum duration of an hour for the entire day). That seems reasonable. It's tiring, so you have to do more than just a quick recovery break to get them again. After a good meal you're OK for a couple more.
But why a hard limit? Instead I've added that you can use it additional times even if you haven't regained the ability yet. But you have to make a Constitution save or suffer a level of exhaustion as a penalty. I use exhaustion for injuries (caused by criticals) as well, and there are other potential reasons why it comes up. So they aren't taking that penalty lightly.
Ilbranteloth