A Ju 52 cannot haul what a Me 321/Me 323 can. The Me 321 were specially designed for heavy cargo drops to be used alongside normal gliders. I don't think any other transport of the day could ship in a medium tank or a heavy AAA + halftrack. As such they did what they were intended to. In the course of the war they were probably used for duties were it may have been wiser to use Ju 52s, but that doesn't make them worthless imo. The huge guns like the Karl were specialized siege weapons and arguably did their job too, e.g. at Sevastopol. Neither of these were ever intended for the same purposes as normal transports or normal field cannons. In my opinion the negative effects these systems had on the German war economy is a bit hard to quantify and could very well be exaggregated.Another thing that I think also helped, was the Germans fixation(?) with giant, sometimes useless machines! How many Ju 52 can they have done instead for the Me 321/323, those huge guns like Thor, Odin etc, made the He 177 into a proper 4 engined bomber from the beginning instead for that with two coupled engines etc., etc...
The He 177 is a different story. It is too bad for the LW that they tried to make their coupled-engines thingy work instead of going the less stubborn but ultimately successful way the RAF went with the Manchester.