I think most people posting on these many threads (some of whom are only lurking now or only check in once in a while) find no fault with the investigation.
That's just my perception, though. I don't see any flaws in the investigation and I work in forensics. There have been some extraordinary claims made about the DNA analysis, but given the facts we have, I think they knew exactly what they were doing.
The very fact that they brought in Amido black (appropriately) should be a more frequent point of discussion. Yet, every time we start to talk about the why of this decision, people get hung up on their being only "one" latent footprint. It's physically impossible for there to be only one latent footprint, but the others probably turned up with a more standard analysis (I don't think they used luminol - I think it was a similar product). When luminol turned up prints, the prints gradually faded (would love to know where they started - I assume at Xana's room).
So they went to Amido black to see if they could find the route taken by this Vans-wearing person as he went to the exit. That means they also have the gait impression of this killer, as well as his shoe size and overall foot impression (forensic footprint work is awesome and an entire subspecialty with experts in various places, one of whom will likely have already weighed in on what is known about the person from their footprint).
This information is, IMO, already in the hands of the Defense who would surely look carefully at it and file a motion if the shoe size was wildly off. It's not wildly off, IMO.
LE, FBI and other investigators/lab professionals are not prone to making tons of mistakes and I can't think of any publicly reported mistakes.
IMO.