In the third movie, Wesker says to Dr Issacs that he expects a report within a week despite it being obvious that that's not nearly enough time, now later on in the movie Issacs finds Alice, Wesker basically says screw you, despite tests using less viable blood actually working in a fashion, in other words with pure Alice blood the cure would probably work, so whats up with Weskers attitude to someone who is clearly a mad, but competent scientist, with a possible supercure?
The final movie, somewhat, clears it up, they already HAD a cure, but unlike Clone!Isaacs, the real Isaacs had a cure that would wipe out the T-Viral creatures, not "domesticate" them, which isn't what Umbrella High Command wanted, until Clone!Isaacs overstepped, they probably would have let him continue tinkering.
She lives!
In Extinction, at the end of the movie, we are shown that Alice survives, thanks to her clone waking up. After promptly telling off the Umbrellaheads, we are shown that there are loads of Alice clones in there. But, if Dr. Issacs really WAS making modifications to the clones to try to make a cure for the T-virus, why would he have an extraordinary amount of Alice clones on hand? You can't make modifications to them without exposing them to the T-virus, in which case, since the clones are imperfect, given that the entire movie is about Umbrella trying to catch the original Alice, will probably just make more zombies? Fridge Logic indeed.
Dr. Isaacs wasn't trying to create a cure for the T-Virus, that was just his lie to the Umbrella heads. He was trying to make himself a loyal army which he could use to beat the crap out of the zombies and take over the world. He wasn't infecting the Alice clones with the T-Virus, he was sending them into Battle simulations to try and re-create the perfect soldier. In fact, they seemed to be immune, as many of them were gnawed on by zombies and thrown into the outdoor pit without resurrecting. The fast zombies that he used to kill the survivor convoy was his backup plan.
How can we make Alice seem more awesome, even at the cost of all the rest of the plot?"