Boris Gudenuf
Deity
IMO the answer is as follows
Railroads, the infrastructure of trade in general
The UN
A well designed Industrial Revolution
the Human Rights Revolution
a meaningful Space Program
Vassal States, being that the English Empire became what it is by having vassals and that's just flat out not in the game, complete with colonies.
1. Railroads - absolutely agree: their exclusion and the exclusion of their effects is a major Defect in the late game.
2. The UN - I would be a bit more general: International and Multi-Civ Agreements: because a recognition of 'International Law' and Collective Agreements predates the modern UN by centuries - see the Law of the Sea from the late Medieval Era, or the Hague and Geneva Conventions, or the Congress of Vienna: the game is missing a lot of Internationalism the addition of which would add much to the Diplomatic Game.
3. Human Rights Revolution - I would argue that increased regard for Human Rights may be recognizable in the late 20th century, but the continued incidence of Human Trafficking and outright Slavery, and violations of basic human rights by almost all participants in the wars of the late 20th - early 21st centuries indicates that the 'revolution' is still in progress if it is progressing at all.
4. Meaningful Space Program - define 'meaningful', because IMHO, there is no such thing in the real world. Virtually all the current 'space programs' are focusing their money and energy on 'space' to augment what can be done on and to Earth: communications, surveillance, etc, or 'raw' research - trying to find out what we don't know. The actual exploitation of 'space' has been much talked about and of course, been the subject of millions of words of Science Fiction, but in practice, has turned out to be much more difficult and far, far more expensive than expected. I can remember reading science fiction stories about individuals and companies setting up colonies and space stations, and people living in such, but the practical problems of human engineering and financing haven't really been solved yet. The current (and previous) Civ model of 'Going to another planet' as a Science Victory is, in fact, Science Fiction at this point.
That's not a Bad Thing in and of itself, but perhaps it means that the game needs a different definition of Science Victory with an alternative Science Fiction Option including specific 'Future Techs' like Nanotechnology and Fusion Propulsion to enable an Alternate Science Victory of space travel.
5. Vassel States - Uh, no, that's not how the English Empire was governed. English colonies were centrally governed and controlled from England, a system so unworkable that every single one of its colonies became separate so that what "the English Empire is" - is that it isn't anything any more. 'Vassels' were political entities connected by family or marriage to a more powerful Sovereign, and came to refer to any political entity whose sovereignty was all or partially under the control of another political entity. In practice, that usually meant eventual revolt or absorption, as in the Netherlands versus Spain or the non-Russian 'Socialist Republics' of the USSR - which became really independent states again when the controlling political entity collapsed, but had a prior history of revolt before that.
I do agree that the game needs more variety of Diplomatic Relationships, especially with City States, in which Suzereignity is ill-defined and incomplete and short of that there is only economic advantage, nothing political or diplomatic. There should also be much more variety of interaction with 'Barbarians' and a variety of both economic and diplomatic agreements/interactions between Civs. Getting back to your first point, there were international agreements to build or connect railroads between nation-states starting almost as soon as railroads started being built, and international cooperation in building major communications/trade infrastructure has become almost the norm (see the Chunnel, for example, or the International Pipelines throughout the Middle East and from Russia to western Europe and Canada - USA).