The problem with the German Navy as a whole was that time was always against them. Deutschland class ships were hybrids because of a reason. The Germans didn't have cruisers or commerce raiders in mind when they drew those ships in late '20s. They wanted battleships, or at least something with similar firepower but light enough to bluff off the treaty limitations just a little bit. This is where the innovative features of these ships come in. They reduced about 15% weight by arc welding instead of riveting. Armour thickening was impossible without substantially increasing the dead weight. The Versailles Treaty set the limitation as 10000 long tonnes, whereas Deutschland was slightly above 12000, Admiral Scheer was about 13600 and Graf Spee around 14500. Fully loaded she weighed about 15-16 KT.
The choice of gun caliber is a dead giveaway that they weren't making cruisers. They would go on to use the same gun (slightly upgraded) on Scharnhorst Class battleships. The choice of propulsion may appear stupid. However they were already playing with diesels in merchantmen. Even Auxiliary Cruiser Kormoran and tanker Altmark had the same M.A.N. diesels. These were not stupid choices for the time. It's simply unfortunate that they couldn't find enough time or patronage to modify the design to be more reliable and efficient. Yarrow and Admiralty boilers had a litany of problems when they were first introduced. Circulation problems, boiler tube failures, superheater underperformance etc. to name a few. The only difference is that unlike the Germans, the British constructors had smarter, less rabid patrons and more resources in terms of materiel and time.
Deutschland class ships weren't intended to fight WW2. Heck, they weren't even Kriegsmarine ships to begin with, they were Reichsmarine ships. They were just good tech demonstrators of a navy that had lost everything a decade back and wasn't willing to let it's engineering and shipbuilding prowess to be flushed down the toilet. They had to find a way to use them once things started to go south, hence the commerce raider thing. And even with those limitations, they had excellent gun control and rangefinding. Exeter got the taste firsthand.
The ships Germans made for armageddon wouldn't start appearing before 1935, by the time Hitler's Nazi behind was safely spread across the red leather couch in the Chancellery. All of them had B&V steam turbines for propulsion and all Versailles Treaty conditions had already been substituted for toilet papers. Therefore, although a trio of weirdos in WW2, the Deutschlands were by no means bad ship designs keeping in mind the time they were built.
As for the Invincibles (or Indefatigable or Queen Mary), their legacy of instantaneous salvation from German salvos was proudly carried on right up till 6 o'clock in the morning of 24th March, 1941 by none other than their younger but heavier sister. Graf Spee fared far better than those Royal junks. And those numbers mean nothing. First of all Invincibles were way heavier, with about 17500 T of design weight and above 21000 T fully loaded. Their propulsion was medieval compared to what was on board Graf Spee. 31 boilers spread across four boiler rooms driving four direct drive steam turbines which could churn out about 45000 shp when pushed to their absolute limits. Deutschlands' dirty diesels could easily make 54000. Don't get me wrong, it was an excellent propulsion system back in mid 1900s but not comparable to the ones used on Deutschlands. In terms of range and cruising speed, the Invincibles (3090 nmi at 10 knots) come nowhere near the Deutschlands (16300 nmi at 18.7 knots). Similarity may be observed in the bore width of the main rifles. Even there, the Deutschlands fired lighter shells with slightly greater muzzle velocity and range. Gun layout, turrets and auxiliary armament were totally different. The only similarity was in armor. The only difference was that for the Invincibles and their successors, cardboard armor was a matter of choice whereas for the Deutschlands, it was a matter of compulsion.