If you would like me to point out something more specific about their boats quality issues, consider reading the IMMARBE Report on the Peter Hughes Wave Dancer. It points out several safety/quality issues with their operation.
17 passengers and 3 crew members lost their lives. Partly due to the way the boat was handled in a storm.
In many folks opinion, if Peter Hughes is going to stamp his name on the side of the boat, then he should hold them to higher standards.
How he handled(snubbed) the survivors and the deceased (and their family) after the accident regardless of who owned the boat is enough that I will never book a trip with them.
I've read the report. I think anyone who has been diving more than a few years has. The problem I have is making the link between the report and "their operation," by which I assume you mean all Peter Hughes boats. The problem, as you raised, is that the Wave Dancer was a "franchise" operation. The safety problems on that boat don't tell me anything about the condition and preparedness of other boats.
I think there are two generally relevant lessons in the report. First, an inexperienced captain can kill people. Second, a captain who doesn't feel he can make necessary decisions on his own is a danger. In light of these two lessons, if I could, I would only book on boats that are owned by their captains--assuming experience and a good reputation. The problem is that, in the places I want to go, most boats are not captained by their owners. In remote locations, there are relatively few such operations, and sometimes the itineraries and schedules of those few operations just don't work for me. So rather than avoiding those locations, I try to look at the others' experiences on those boats. I've found that to be the most useful, though hardly foolproof, approach.
As to Peter Hughes, I know some people are furious with them over the way the Wave Dancers' survivors and family members were treated. I don't really know just what happened. There is no authoritative report on this the way there is on the accident itself. There are only the views of those affected by that treatment. I imagine that if I were the family member of someone killed by the negligence of the boat's captain and owners, I would want their heads on a pike. I can't even imagine their pain.
However, having said this, if I were to die on a dive trip, I would expect any operation's owners to stonewall, obfuscate, rely upon their extorted waivers and blame me for my death--if they thought it was in their corporate interest to do so. Corporations are by definition amoral, driven by profit, not by any desire to do the right thing. So while I appreciate the views of those who say they would never dive with any Peter Hughes operation, that's not my view. If a particular boat has a good reputation and gets good reviews, I'll consider it if it otherwise meets my needs.
I'll report back after our July trip to let everyone know whether this was a good or bad decision in the case of the Star Dancer.