People would have eventually turned on it and nitpicked every detail...
Then we would have fun threads like, HAS FIREFLY JUMPED THE SHARK?, Firefly is dead to me, Character X needs to die!
If the show had run for 5 years we wouldn't have got Serenity, so I'd discount those events. I would probably keep the blue hands men in for two or three seasons, Reavers would not be from Miranda and probably just be mysterious and deadly, keep to the maurading monsters of craziness
River wouldn't be so uber so soon, stretch it out. That mobster guy that looked like he might have died comes back to terrorise the crew. Definitely go into Books past but he doesn't leave the ship. Inara does but comes back in season 2 to save Mal or Simon/River.
One of the season finales, maybe 2 or 3 I'd blow up Serenity
. Obviously they'd need to get a replacement and the crew would disburse and you'd need some crazy plot to pull them all back together. Include other people like River either some on the run, some "failures" or some working for the alliance. Maybe even have an arc where River is working for the Alliance during evil or whatever the Alliance does.