The reason why Blissey is not completely outclassed by Chansey is this:
252 SpA Life Orb Thundurus Thunderbolt vs. 252 HP / 4 SpD Blissey: 142-169 (19.8 - 23.6%) -- possible 6HKO after Leftovers recovery
While Chansey do this
252 SpA Life Orb Thundurus Thunderbolt vs. 252 HP / 4 SpD Eviolite Chansey: 121-142 (17.1 - 20.1%) -- possible 5HKO
There are three reason why Blissey is an advantage position over Chansey:
-Because Blissey can switch in random Knock Off from pokemon like Thundurus, Deoxys-S or Mandibuzz without being that crippled, because Blissey loses 6,25% of recovery, Chansey loses 33% of her defenses.
-Blisseys take 6,25% of recovery with leftovers. Meaning that she works equal or better against a lot of special attacker (the pink blobs are special walls) only because of them. This also means that Blissey is better against Tyranitar and Hippowdon Sand Stream (they are in a respectable amount of teams), Burn (only 6,25% and after Leftovers), Poison (standard poison does only 6,25% and toxic posion does 6,255 net less every turn), Leech Seed and entry hazards like Stealth Rock.
-The surprise of having an coverage attack in his arsenal, that can give some surprises to some threats that think Blissey is a free switch in. Chansey has no opportunity doing that.
The case of Florges is different: The only thing Florges has is better speed. But Sylveoin can pass higher Wish (HP is the key stat since Gen V to pass Wish), has better physiucal bulk (higher HP and identical defenses) and his special deenses is only worse by 2%. And that pixilate Hyper Voice with higher net BP and bypassing Substitute is great.
Note that Grass (what Florges has) is an horrible coverage type to Fairy while Sylveon ghets Ghost coverage which is almost perfect neutral coverage. And Florges can't pass anything to anybody.
About Machamp vs Conkeldurr, the only thing Machamp has over Conkeldurr is Dynamicpunch and a bit better special bulk while loses physical bulk, priority (has Bullet Punch but this is weak), a 100% viable Assault Vest set thanks to that And Drain Punch (Machamp can't learn it) and a bit more attack.
And about Donphan, it's a more complex case than you might think. Technically it's outclassed by four pokemon:
Donphan is only used in the mid-high ladder for people who want a bulky spinner (at least fro the most common physical side) that doesn't take a Mega slot and doesn't have glaring weakness.
-Excadrill, but has 3 desirable weakness that are commonly physical in OU that Donhan doesn't have.
-Mega Blastoise who has better defenses and Rapid Spin and offensive presence but Blastoise can't be paired of 2 of the three big reason to run an spinner: Pinsir, Charizard and Talonflame.
-Hippowdon, who is better physically and way better specially, has the annoying Sands Stream and the option of Sand Force if it hinders your team and has reliable recovery. But doesn'0t have Rapid Spin.
-Landorus-T: Has a similar type with similar weakness and overshadows it in the defensive role thanks to Intimidate, apart of 145 Base Attack. But doesn't have Rapid Spin.
There are another case of overshadowed Pokemon like Jolteon vs mega Manectric and Thundurus; Arcanine versus Entei and MCharizard X.