The Fairy-typing, to me, seems to be added to Pokemon that are supernatural in appearance but aren't Ghost or Dragon - that's why not adding it to the Vanillish and Klink lines was such a miss IMHO. Plus, a fast Steel/Fairy would have made an interesting contrast to Klefki.
Unpopular opinion: I think they should make SIGNIFICANT changes to the balance between various typings in what's SE and Resist damage. A lot of the stuff in there is weird legacy items without much consideration for an actual metagame, and it woulda been hard to have a 'sensible' balanced count of what resists what because with 17 types you have an odd number, making the math impossible as to what should be what.
The reason that Bug (as an example) sucks is because it's SE against three and NFE against seven! Not only that, Bug types have hilariously low BSTs as well.
Typings should be separated into Defensive and Offensive categories, with Defensive having more resists but fewer SE, and the converse true of Offensive. Defensive types might be SE against 3 types and Resist 4 types, with the pattern reversed for Offensive. Exceptions could be made if you add an Immunity, but whether that adds a buff to the attacking type or adds a debuff to the defending type is up to the game balancers. The Flying immunity to Ground, as an example, might give Ground an additional SE hit against another Type, or add a weakness to Flying.
I also think that one type should be categorized one type as super-defensive (Steel), and another as super-offensive (Fire or Fighting), that trades its resists or SE hits for its super typing. This would modify other Typings without impacting THEIR internal balance - Steel might have a Bug resist, but that wouldn't add to the overall SE/NFE balance of Bug's list.
As an example, rebalanced Bug would be Offensive, SE against Dark, Grass, Psychic, Fighting and Resist Grass, Ground, and Psychic. I'd have to spend some time on the math of this, but balancing the typings would make a lot of damned sense.
If only Game Freak didn't have their internal policy about making serious changes to the game... that does seem to be changing, though, so fingers crossed.
Another unpopular opinion I've expressed before is the notion that they should do a serious cull of both redundant Pokemon lines and redundant moves that do the exact same damned thing. Do we really need FOUR Normal-type moves that "Lower opponent's Attack stage by 1" or "Raise user's Defense stat by 1"? Also, take duplicating Pokemon lines like Unfezent or Swellow and shoot them in the head.
Less trollbaiting, actually examine what each Pokemon line adds to the game and either keep or cut it - Staraptor versus Pidgeot, for example, is a "Physical versus Special" split of offensive bird types, so worth keeping. Alakazam versus Reuniclus, is a "speedy attack versus defensive" choice, so interesting and worth keeping. Muk versus Garbador? Little difference in their movepools, little difference in their BSTs, so look at which one is a better design and cut the other.
I'm not talking about judging just by battling capability, but by niche, fanbase, and unique design. Seriously, is ANYONE a Mothim fanboy? Did you forget until I mentioned it that it even exists? Or would anyone remember Dustox/Beautifly if it wasn't such a pain in the butt to get both for a Nat Dex? But Rapidash and Zebstrika are both horse-types with different designs and typings, so both would be kept (despite neither being anything but NU tier).
Gen 5 is the worst culprit, but all generations til 6 had the problem of "Adding new pokemon of old types just because it's a new region, yay!" It WAS fine back then, don't get me wrong, because it made each new region seem real and new, but now we're over 700 new types of Pokemon, and it's just going to be too big in only a few generations. I mean, in ten years (going by Pokemon Generation = 3 Years), even adding a modest 80-100 Pokemon we'll have over 1,000 different Pokemon counting Formes and Megas. Ten years is not a long time.
Storyline-wise, justifying this by a long-term time skip and saying that some pokemon combined lines by convergent evolution, and having caught Pokemon count for both parts of a Nat Dex entry (example: Garbador being #089 and #569) would be fascinating. Plus, wouldn't you like to meet Professor Bianca, or challenge Pokemon Champion Brendan?
It would piss off people, to be sure, but it would make the whole game healthier and keep Pokemon viable for longer. The sooner done, the better it would be.