I've only played the first two, so I'll list my least favourites from both of them.
Flygon- It speeds around the screen at an unbelievable rate and is extraordinarily hard to catch up to.
Salamence- You have to draw 50 or more loops continuously without the chain breaking while avoiding its attacks. Forget Steelix, this was the hardest capture for me.
Steelix- It was still hard, though. It moves too erratically for it to be an easy boss.
Shadows (note: I have never fought Regigigas, so it will be exempt):
Rampardos- It was more in my childhood, but I could never defeat it without having to capture more Pokémon for their Poke Assists. Funny thing is; in my last playthough, I found it extremely easy.
Drapion- Same as Rampardos and for the same reason: I had a hard time defeating it, and when I finally did, my wrist was aching from the pain of so many circles and so many failed tries. I think that time was luck.
Bastiodon- I genuinely hate fighting these. I find their attacks unpredictable and deadly, even in the overworld.
Friend Safari: Sunkern, Sawsbuck, Maractus