It might be because it was still technically early in Sinister’s life as far as cloning goes. He does get it right by AvX with the Maddie Clones that take the Phoenix Five’s power briefly. His first clone recorded in comics was a Namor Clone back in WW2. I surmise his Bar Sinister was created before Maddie also, but honestly, I don’t remember if there is real evidence of that. Even so, Maddie is technically his first attempt at cloning an Omega Level Mutant, so that also ought to be a hurdle he had to learn as well.
Yeah, all things considered, Maddie is kind of an anomaly in his cloning experiments, since they were all relative successes in how close to the original they were genetic wise and potential wise.