Much about Alma's mansion makes sense when you remember that she's an Eco-Terrorist, from both the "eco" and "terrorist" sides. The solar panels on the roof are a great source of renewable energy, and also reduce the odds of a utility worker finding something he or she shouldn't. The house's large windows are great for letting in natural light and also for keeping an eye on the outside. Even the location on a virgin beach fits: aside from the obvious benefits of living in an out-of-the-way locale, it might also help to block development and the like there.
The Shadow Client's obsessive hatred of Providence makes a lot more sense once you realize that they were The Man Behind the Man for the super-agent program which produced both 47 as well as Lucas Grey himself.
The very specific story which Janus tells to Agent 47 about Doctor Ort-Meyer seems like a bit of randomness until you realize he explictly says that he recognizes 47's look as well as eyes. In short, Janus is Defiant to the End and just wants to insult 47 until he's executed.
The meaty bone item you can find in Santa Fortuna may seem harmless until you start to wonder what it belonged to, and then you realize that Rico owns a man-eating hippo. Worse yet, you can find one in the mansion kitchen.
The original trailer for Hitman had the Shadow Client talk about how 47's executions had resulted in the rise of new people due to the Evil Power Vacuum he created, which we now know is Providence. How is eliminating Providence going to do anything but repeat the process? Perhaps with something worse?