I mean if Roosevelt supports the Peonage trials further and then backs off like he did IOTL, you have a disaster for blacks in the South, as it would be a shown as a fact that Blacks were being kept in Peonage and worked to death in mines and then the Government chose to do nothing about it when caught. Thats a great way to shatter a legacy right there.
Never mind all kinds of talk about Eugenics, War-mongering, the ability for Taft or another Post-TR figure to actually be seen as a progressive Trust-buster as opposed to Roosevelt, the fighting with Mark Hanna damaging his standing in the Republican Party, fighting with JP Morgan threatening the economy especially in 1907, the New Nationalism being put into effect, and being seen as a clear power grab by Roosevelt...
The man is far from perfect, no matter what the fandom says. Its easy to turn him into something less appreciated. Look at Jackson, look at Grant, look at LBJ. There are plenty of people who have smeared Great men and dragged them down, no matter what their victories and positive attributes were. Teddy is not immune, and is in fact more vulnerable then most.
I'm not sure whether making Roosevelt less appreciated or even an object of condemnation fits the thread title, which implies making him a rival for James Buchanan for sheer awfulness, which is considerably more difficult than making him an early version of Lyndon Johnson or a later version of Andrew Jackson.
With that said, I think you've mentioned a number of ways to prevent Theodore Roosevelt from being an idealized President, and even a subject of condemnation by future historians. Aside from what you've mentioned already, may I suggest another option? Roosevelt never makes his comment about not running in 1908, and when that year comes, rather than standing aside, he actually runs and wins another term in office. As Mikestone has pointed out on numerous occasions, the Republican Party was in many respects in trouble in 1912 even without TR's third party run. And with TR still President, it's not all that hard for me at least to imagine a progressive movement that's opposed to Roosevelt, or at least believes that he doesn't go far enough. Someone else is elected President in 1912, and that President is seen as the "real" progressive in comparison to the demagogic, but ultimately conservative, Theodore Roosevelt. I know, that doesn't exactly make him a horrible President, but it might make his long term reputation more akin to that of McKinley and Taft than his reputation today, indeed, he might have a slightly worse reputation, given what could be perceived as an outright power grab in 1908. Most people don't criticize FDR for running in 1940, because there was the Second World War on the horizon to justify such an unprecedented run. In 1908, as far as I am aware, there wasn't any similar sort of crisis underway that might justify what would be in effect a third term. So Theodore Roosevelt would be someone who couldn't stand aside, and who spoke of much an accomplished far less than his hypothetical successor. Then, either somehow avoid the Great War, have it end in 1916, or have Roosevelt's successor lose the election of 1916, and have his successor blamed for the almost inevitable excesses associated with American involvement in that conflict.
Alternatively, you have another option. Have him bite his tongue and stay out in 1912. Taft still loses, and in 1916, Theodore Roosevelt is able to win the nomination, and narrowly defeats President Wilson to return to the White House. Here it's TR who brings us into WWI, it's TR who is responsible for the war-time excesses that are a large part of the reason why a lot of posters here absolutely despise Woodrow Wilson.
Ah, but then I've only made him another Wilson, I probably haven't done enough.