Except that if the Empire had had spore drive, the Alliance could probably never have conquered it.
In real life, sure. But in Star Trek, whenever a new technology turns out to have a problem, it's completely abandoned and never heard from again -- multitronics, soliton wave travel, subspace transporters, you name it. The one exception being holodecks, which they kept using despite constant problems because they were built into the format from the start of TNG. The status quo rules, scientific logic be damned. That's doubly true for a prequel.