CapnZapp
Legend
I don't think using HD to equate to level in any fashion will work. Let's take a look at an example:
- An orc and a gnoll are both CR 1/2 monsters, meaning they are roughly equivalent in ability.
- The orc has 2d8+6 Hit Dice (due to 16 Con)
- The gnoll has 5d8 Hit Dice
With a spread like that (2-5), how can you equate HD to levels?
Rather than driving yourself crazy with the math, why not level the NPCs as needed? If the party is looking weak in a fight, bump up the NPCs a Hit Dice or so, or give them another +1 to hit. If the party is weak on spellcasters, give an existing NPC spellcaster either more spells or another slot at a higher level.
Rather than trying to be exact, and compare yourself to a scale that doesn't exist, make it easier on yourself by giving the PCs what they need (or what you foresee they might need in a future encounter).
You can't know this but I don't use CR. I believe it is inaccurate to the point of being useless. (The how and why we can keep to another thread) In this context I would very much like not to have to calculate Challenge Ratings. While the monster entries already have CRs listed, if I based levelling on CR I would have to re-calculate CR to keep a creature's CR current as it levels up, or I won't know when it is time to level up the next time.
As for driving myself crazy, thanks for your concern. Level as needed is a fair suggestion, though I would miss having some crunch, even if it would be pseudocrunch only...!

And to that end, if something would drive me crazy, it would be to use Challenge Ratings...
For starters, level 1 would correspond to something like CR 1/8. CR 1 is more like level three or four. But I'm gonna stop there.
To be fair you've confused CR and HD in your example above.
The Orc would be, per OP, a 2nd level creature and the gnoll a 5th.
Perhaps you could hybridise it:
- starting level equivalent is HD/2
- level progression is based on HD/1
- thus your 6HD Spy would have the abilities of a 3rd level character but would require the amount of XP needed to go from Level 6 to Level 7 before he gained his "actual" 4th level equivalency.
Would this satisfy OPs need for slow advancement combined with simple yardstick of abilities?
Well, I am not confusing CR for HD at least, not sure if you meant me.
As for your example, I'm afraid you (too) might be having it backwards: what does "your 6HD Spy would have the abilities of a 3rd level character" even mean? What is a "actual" 4th level equivalency?
But let me stop you right there, because what happens when you level is a given: you gain a hit die; you gain an ability increase at levels 4, 8, 12; your proficiency bonus increases at levels 5, 9, 13. Etc.
What this exercise is about is simply finding out WHEN to level. I don't want to mess with the stat blocks beyond that.
So to interpret your hybrid example the only way I know how:
- starting level equivalent is HD/2
- level progression is based on HD/1
- thus your 6HD Spy would have the abilities of a 6HD Spy but would count as a level 3 (6/2=3) creature for purposes of levelling. Thus require the amount of XP needed to go from Level 3 to Level 4 before he gained his 7th Hit Die.
I have marked the changes in bold. Not sure if this is what you meant. If so, thank you - now I understand. Otherwise, feel free to respond.