I have been hesitant to join this discussion, since paint and colour is such as subjective issue and the topside colours of Victory are an especially fraught matter. The recent pinkish buff is certainly an unpopular choice with virtually everyone, in part because the ship has been black and yellow for the last century and that is the abiding impression everyone has had all their lives. But I think I need to stand up for my colleagues in the preservation trade, who get pilloried in this question on a regular basis for doing their jobs. So I would like to make a few points about how we do this kind of research and why, as well as some specific challenges with Victory.
1. As preservation and research professionals, it is not our job to reinforce or confirm widely held beliefs. Our job is to follow the evidence, where ever it takes us, and report the results accurately. We do this knowing that every time we provide a new view of a widely accepted idea there will be some backlash. Partly we do this to inspire people to think about things rather than accept them blindly. If nothing else, that horrible pink (which I do not like any more than anyone else does) has made a lot of people much more aware of how we study painting history on historic structures. Just because paintings and model kit box tops have portrayed the ship a certain way for decades does not make it true, and if the actual evidence of how it was painted exists, we should try every technique we have to discover what the reality was.
2. Paint history analysis is not voodoo or guesswork, it is a well developed, scientific research process that has been proven on numerous projects over many years, from individual pieces of furniture and paintings to entire buildings. It consists of three parts: scraping or sanding through all the paint layers back to clean wood to reveal how many different layers are present, tying one or more of the revealed layers to specific times or events, and chemical and microscopic analysis of the layers to identify the pigments (and an appreciation of how they might have appeared). This has been used to reveal orginal compositions of reworked paintings, the aesthetic history of buildings, and the original finishes of objects with long lives. We have used it on Vasa to reveal the original colour scheme, which turned out to be be very different and much more garish than people had thought. The results are often surprising or unsettling; people who are used to the dark tone of many Old Master paintings are put off by their bright appearance once cleaned of later varnish that has darkened with age. To them an Old Master painting has a dark, brownish tone, but that is not what Rembrandt painted.
3. Ad hominem attacks on the people who are trying their very best to do the right thing is not very honourable. If you disagree with the results of a research project, please bring a good argument, based on the evidence, to the discussion rather than rubbishing the qualifications of people you do not know. As scientists, we question our conclusions all the time and are always looking for more and better evidence. Most of us are not wedded to our conclusions at the cost of reason, but want to know the truth. The people who undertook the study of Victory's painting history did not do so for the purpose of making people angry, they employed the standard techniques used on historic structures with the goal of developing not just a paint scheme for Trafalgar, but a comprehensive painting chronology that is part of a much larger study of the ship's entire history. And before you go down the "scientists are often wrong" route, think about two things: scientists brought you the cell phone you might be reading this on, and if you had to have a brain tumour removed, would you rather it was done by someone with a scientific education or the local carpenter who happens to have an interest in medicine? Scientists are often wrong, that is part of the job, but real scientists are constantly learning and understanding why they are wrong in order to get to the right answer.
4. As others have pointed out here, H.M.S. Victory has been a lot of different colours over the years, even during its operational career, due to changes in Royal Navy practice, individual preferences by commanding officers, variations in paint formulation, etc. This is before one considers changes in the paint over time due to abrasion, U/V radiation, weathering, interaction with other coatings, etc. Trying to replicate a painting scheme for a specific event, which is the expected path for this ship because it is so closely tied to a specific battle, is an extraordinary challenge. Victory may only have had the Trafalgar scheme for a matter of weeks or months, but was painted and repainted in other colours over much longer periods. Trying to pin down one particular scheme is a complicated task, especially if you consider that we are not just interested in the big picture colours of the background and gunport bands, but need to understand the entire colour scheme and its details. It may be possible, for example, to recover the original colour or the colour of a specific item at a certain date because that item has been preserved, but finding enough bits of evidence from the same target date is a challenge. On Vasa, in contrast, there is only the original paint scheme and all of the original timbers are preserved, so our challenge is a walk in the park by comparison to Victory.
5. Very little original surface from 1805 survives. The ship is now more than 250 years old, and has been under near-constant repair, alteration, and restoration. The ship was extensively repaired almost immediately after Trafalgar, losing substantial areas of the planking, and later repair and restoration efforts have continued to remove what one could call the Trafalgar surface. At the start of the current restoration, it was realized that not only was very little of the upperworks original to the early 19th century, but much of it (including almost all of the exterior planking) dated to 1955 or later. Even where old, pre-1955 timber survives, it is a challenge to assign it a year. This is a fascinating detective story. In a few cases, the installation date of a specific timber or structure is known, so the first colour applied to that timber can be dated exactly. This provides a benchmark that allows the construction of a paint chronology, which then can be used to identify which timbers are earlier and which ones are later, as well as giving an indication of the general trends in colour choice. It can also allow the correlation of paint layers on different objects, so it is possible to say something like, when timber A was painted green, timber B was painted red, then both timbers were later painted black. With a little luck, it can be possible to build up an overall paint scheme for a particular period, especially in later years when the ship was photographed. The people working on the ship have also used dendrochronology (tree-ring dating) to determine when certain timbers were felled. This has had some unanticipated and disappointing results, such as showing that the famous "Nelson knee" against which the admiral supposedly died, is from a tree cut down many years after Trafalgar. On the other hand, the research has also shown that some parts thought to be later restorations or anachronistic are actually from the working life of the vessel. The restoration project has produced a number of maps of the structure, which show the construction and restoration history in graphic form. It is a fascinating story, but the Trafalgar surface has proven elusive.
So please understand that the people doing this work are passionately committed professionals in search of conclusions based on real evidence, they are not idiots or misguided, incompetent bureaucrats. Their goal is not simply to replace rotten timber for another round of repairs, but to identify and conserve as much of the ship's historic structure as possible. The challenge they face is extraordinarily complicated and their audience is dedicated and quick to criticize. They are using the most effective research methods available and often pushing the edge of the envelope, developing new techniques where none existed before. The archaeological mapping of the hull structure, for example, is one of the most comprehensive documentation projects I have ever seen, and once complete will provide a definitive construction, repair, and restoration history of the ship. It will likely reveal a great deal that may surprise people, not just the change to an unpopular colour.