Pokémon games in order of werster's favouritism! (Note a '>' denotes how much more favourable the game is compared to the next :))
[This is from a casual standpoint. Speedrunning standpoint is below]

Pokémon Crystal 
>
Pokémon Heart Gold / Soul Silver
>
Pokémon Gold / Silver
>
Pokémon Black 2 / White 2
>>>
Pokémon Red / Blue
>
Pokémon Yellow
>>
Pokémon Emerald
>
Pokemon Platinum
>
Pokémon Omega Ruby / Alpha Sapphire
>
Pokémon Black / White
>
Pokémon X / Y
>>>>>
Pokémon Fire Red/Leaf Green
>>>
Pokémon Ruby / Sapphire
>>>>
Pokemon Brilliant Diamond / Shining Pearl 
>
Pokémon Diamond / Pearl
>>>>>>>>>>
Pokémon Scarlet / Violet
>
Pokémon Sword / Shield
>>>
Pokémon Ultra Sun/Moon
>
Pokémon Sun/Moon


As for the spinoffs, I don't think it's fair to compare them as the amount of content/replay value is entirely different. On enjoyable level though, most fall around the same as Emerald, and I love most of the ones I've played, including the Stadiums, Snap, Pinball, Mystery Dungeon and Puzzle Challenge.

In terms of the games as speedgames goes...

Gen 4 (DPPt + HGSS)
>>>>
Gen 5
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Gen 1
>>>>>>>
Gen 3
> 
Gen 6
>
Gen 2
>
Gen 8
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Gen 9
>>>>>>
Gen 7


As for romhacks & fangames, there are so many different genre's and directions that it's hard to lump them all together. Especially when a lot of the things people try to do with them, I don't care for at all (I don't care about "enhancement" hacks, "<x> gen in <y> gen", kaizo, "mature" stuff, etc)

Of the ones I've played, the three that I really enjoyed sitting on the top shelf are: Prism, Gaia, and Unbound.