Here’s how I see it: A bunch of ponies started out as only background ponies. As soon as they get semi- or fully-consistent characterizations and voices, or are the subject of an episode, they become tertiary or supporting characters. Minuette, Twinkleshine, and Lemon Hearts are now minor supporting characters, except when they’re used in their original role as background ponies (which still happens, even in Season 5).

@TheAntiCat  

 
Cheers pal. I think about things like this for fun, and it just stays with you for ages (I did forget some characters, and some only occurred to me when writing it :P)
 
The spilt in the secondary tier is something I’ve thought about as well, and I think the villains are a good fit for the minor tier (perhaps with the exception of Discord since he appears more). For the majors, Shining Armour and Cadance, the CMC and Celestia/Luna if you don’t count them as primary and maybe Granny Smith, Big Mac, Zecora and the Wonderbolts. The rest of the secondary characters I listed would be in the minor tier.

@EddersCPFC  
I tried twice last night to write a list like yours but my brain refused to cooperate. Your list is bang on.  
I suppose Secondary could be split into Major and Minor tiers, villains taking the Minor tier.

@TheAntiCat  
Primary - Obviously the Mane Six and Spike, but may also include the CMC and Celestia and Luna  
Secondary - CMC and Celestia and Luna if you don’t consider them primary, Cadance, Shining Armour, Discord, the background six of Doctor Whooves, Derpy, Lyra, Bon Bon, Octavia and Vinyl Scratch, the Wonderbolts, Zercora, Cheerilee, Diamond Tiara/Silver Spoon, Big Mac and Granny Smith  
Tertiary - Minuette, Berry Punch, Twinkleshine, Lemon Hearts, Cloudchaser, Flitter, the mane six’s pets (if you count them).  
Misc - Pretty much any background pony that hasn’t spoke, the mane six’s other family members sans the apples (and maybe the pies).
 
I’d say villain of the week fits somewhere between secondary and tertiary. It’s hard to say because whilst they’ve played major roles, they’ve only appeared at least twice including the Season 5 finale and their respective episode(s). This is all just my opinion though.

@Mr. Horrible  
I suppose the hierarchy goes:  
Primary  
Secondary  
Tertiary  
Misc
 
Now, it’s kinda obvious who the fills the primary section. Moving down is where it gets tricky.  
Secondary are common speaking roles, tertiary are less common roles and Baddie of the Week, misc is well, all those who are just there to fill the void or conveniently advance the plot.
 
Any refinements from y’all?

Just a thought: Do these three technically count as background ponies anymore? I mean they did have a whole episode about them, with official names and VAs and everything.