It mostly depends on your priorities. Do you want the quickest boiling times? Do you want the lightest/most compact option? Or something else?
For me, I like a simple, light, and compact system where everything can fit inside the pot:
Canister stove setup - SP 600 with homemade lid.
My SP Gigapower stove, SP fuel canister, towel, BIC lighter all fit inside the pot. I then place the pot and my spork inside the mesh pouch and cinch up.
Alcohol stove setup - Firelite 550 with lid
My wedding tin alky stove, wind screen, BIC lighter, spork, towel plus up to 4 ounces of fuel all fit inside nicely.