Here is a list of fundamental differences between reality and idealized models of the world. It can provide guidelines when designing virtual worlds, or serve as a checklist when trying to reason about the real world:

Irreversibility.

Some things are more easily done than undone (building something versus destroying it, cleaning something up rather than making it dirty, etc.), and some cannot be undone at all (killing people, losing information, wasting resources, etc.). This means that a small number of wrongdoers can have a disproportionate impact because undoing their mess take so much time, and this implies that preventive measures are needed to limit the occurrence of irreversible bad things. This is in contrast to virtual places like Wikipedia where reverting edits isn't substantially harder than making them, and where you can benefit from the fact that vandals are a small minority.

Low dimensionality.

The world has a small number of spatial dimensions: only two are really usable, the third one is harder to use because of gravity. Because of this, the possibility of interaction is limited: you cannot have a high number of things acceptably close to each other. This holds both for groups of people (large groups of people cannot interact meaningfully in real life, which is an obstacle to large-scale collaboration) and for cities (to have everything close to everything, you need absurdly high density).

Imperfect coordination.

Even with arbitrarily good communication technology, large groups of people are harder to coordinate than small groups, because of cognitive limits. For this reason, whenever two groups have contrary interests and must hold one against the other, the larger group will be disadvantaged and have much higher risk of defection. This is a factor explaining why the masses have a hard time coordinating, even though they are numerous by definition.

Non-autonomy of children.

While the harm principle dictates that consenting adults in isolation can be simplified out of the moral equation, this does not work with children: adults in isolation can have children, and those children will not be able to legally consent to everything their parents might do to them. For this reason, society has to keep an eye on how parents raise their children, and find some compromise between the parents' rights and the child's.

Necessary infrastructure.

Long-distance communication is not a given but depends on artificial infrastructure which is not free, can fail or can be controlled by malicious parties. You cannot assume that everyone has access to the Internet in the same way that anyone has access to air.

Unbounded vital needs.

If the vital needs of people could be bounded, there would be some hope of managing to satisfy the needs of everyone and assuming that the survival of every human being is ensured. Sadly, people can have arbitrarily complex health problems and could need arbitrarily involved and expensive treatment. This can be dealt with through an insurance system, but complicates things because some people who have simple needs will want to opt out of such a system, making it unsustainable.

Critical mind.

To achieve the independent thought and critical spirit required to be a free, autonomous agent, education is required. People who are not given this education cannot be considered as individuals and it might not make sense to consider that they are responsible for their actions. Yet, they need to be dealt with in some way or other.

Inheritance.

Assume that money represents some measure of social utility, and that people who earned money should be allowed to use it as they like. In this setting, it is a major problem that most people will want to give their money to their offspring, because the money that the offspring will thus inherit is not linked to their social value. The problem is that the individual interests of the donor ("benefit my offspring") are at odds with the interests of society ("allocate money to people who produce value"). There are no solutions except restricting the freedom of people to use their money or increasing inequality at birth because of the parents' wealth.

Physical encounters.

It is not possible to assume that people live autonomously in isolation from each other and only communicate by exchanging of information. People desire friendships, close relationships, and physical relationships. For this reason, they have to meet in real life.

Public-private continuum.

You cannot divide the world in public places and private places and say that there should be no expectation of privacy in public places, because you need to go through public places to travel from one private place to another. Besides, private conversations will often take place in public space with some expectation of privacy between the speakers. I tried to think more about this point.

Repetitive work.

In reality, repetitive tasks have to be carried out. If you want to do the same things multiple times, you will have to do so, and it will usually be complicated to build a robot to perform the task for you. This is in contrast to the virtual universe where things are usually much easier to formalize and automatize, and where the effort required by a task is much closer to its Kolmogorov complexity.

No records.

Even if there is no expectation of privacy somewhere, there is usually no complete perpetual record of what took place there. Hence, there cannot always be an objective assessment of the truth of factual statements involving public data. Note that the problem is not that records are not reliable and can be tampered with, but the fact that they are not complete or numerous enough: the higher the number of independent records, the harder it gets to engineer consistent fabrications. This is in contrast to virtual space where there is usually abundant evidence available because recording something is often easier than not recording it.

[I just wrote this list quickly to dump some ideas I had in the back of my head, it might not make much sense.]