Q:

Why weren't Baden, Würtemberg and Bavaria independent states ever restored, unlike Austria?

The southern german states of Baden, Würtemberg and Bavaria were independent states until 1871. Their historical background is quite different from the northern Germany which was dominated by Prussia at that time. The southern states have always been on the side of Austria and France rather than Prussia, mostly because of their predominantly catholic culture.
Otto Von Bismarck, which was often described as having very strong imperialistic, military and expansionism policy, wanted to annex those states, but the monarchs of the southern states were hostile to that idea. He tricked the southern states to help to defend Prussia against France (that he is accused to have himself provoked on purpose) in 1871, and used their victory to proclaim the German Empire.
Charles the 1st of Würtemberg and Frederick the 1st of Baden were hostile to Prussia's imperialist policy, and Ludwig II of Bavaria was so much opposed that he boycotted the proclamation of the Empire. Which is to say how unified Germany can be seen as an illegitimate state from the very start.
From any time past this unification, it would have been easy for those states to claim they were victims of Prussian imperialism and ask for independence on historical grounds. For example:

After Germany's defeat in 1918, many new independent states, that either disappeared a long time ago or never existed, were (re-)created (for example, Poland after 123 years of political non-existance). It would have made perfect sense for southern German states, which were forcefully unified only 47 years ago, to claim their independence.
After WWII, Germany was completely defeated and ceased to exist politically. The allies re-created the FRG, the GDR and Austria a couple of years later, but were careful that the state of Prussia was dismantled, as Prussia is what united Germany, and is associated with strong military and nationalist culture (and thus, the rise of Nazism). It would have made perfect sense for the allies to split the former 3rd Reich into more sovereign states, based on the fact that Prussian unification is the root of German nationalism and two world wars.
During the cold war, since the United Nations were created, small independent states have almost as much political power in international relations than bigger states, because they have a seat, no matter what their area and population is. Having more than 2 German speaking states on the capitalist sides could have been a good way for the western allies to have more influence against the communist block and in particular the GDR.

Since the territories of the former third Reich were doomed to be split in multiple states anyway (nobody knew that the GDR was going to disappear, and Austrian Anschluss is reminiscent of Nazism), it would have made as much sense to make it split in an historically justified way. What made the Allies separate Austria from Germany, and split off East Germany (mostly the former Prussia) from the rest of Germany, without doing the same to Bavaria, Wurtemburg and Baden?

A:

Splitting up western Germany like that would've weakened western Germany as a counter to East Germany. Quickly after the war the allies saw the benefit of a strong West Germany against the Soviet bloc. This is why the plan to reduce Germany into a pastoral society with massive starvation was quietly abandoned and Marshall Plan aid became a thing instead.
Plus no one asked for it at the time. Maybe it would have been easy to make a case for independent Bavaria, but the case wasnt made.

A:

The structure of post-war Germany was defined by the Allied governments and leaders, not by the Germans. Half of Wurtemberg was in the French zone, the other half in the US zone. This is what Stuttgart, one of the principal cities in Wurtemberg, looked like in 1945:

People were literally building huts out of rubble as shelters. Just finding water was a huge problem. They were in no condition to rule anything or start making claims to stateship. I suspect independent Bavarian nationalism was not really an active political movement in 1945.

