I personally found Skeletron Prime to be the hardest among the three. When I finally got Titanium armor I usually would have Cursed Fire or Golden Shower, I stayed away from the biome Mimics as they are very difficult to fight without good preparations and I really have bad luck getting the souls. When they spawn either naturally or from their summoning items, I always use the natural environment for the battle, yes, no arena.
The Destroyer takes some skills to fight with Golden Shower, and it was lucky that I can get enough mana stars to continue the battle, takes around 6-7 minutes.
The Twins were easy, just fire at them and fly diagonally when Spazmatism is in second phrase, that will cause him to miss most of the time unless your wings expire, just remember to buy enough Greater mana potion and have a mana flower, takes about 3 minutes. Retinazer is just meh.
Skeletron Prime is another story altogether, I can dodge the Prime Saw and Vice most of the time, but that will cause my spells to miss the head. If I try to hit the head I will get hit by the Saw and Vice, even if I summoned him at 7:30 p.m. exactly, I always run out of time, just about ~30 health remaining at 4:30 a.m. Eventually I farmed for Broken Hero Blades and finally brought down the battle with True Excalibur, the battle lasted for 5-6 minutes.