I would concur that the V2 was probably a waste of effort in view of the damage it caused in relationship to developmental costs. Paradoxically, perhaps its immunity to interception was a drawback, because no allied interceptors needed to be repositioned to defend against it.
The basic problem is that virtually all of the German wunderwaffen (rockets, jet propelled planes, the H2O2 submarine engine/snorkel, were all being brought on line after the outcome of the war was basically decided. It is almost ASB to imagine any of these breakthroughs reaching front lines in 1942-43 when they might have made a difference.
Germany would have been best served by adopting full mass-production techniques and placing its industry on a full war footing in 1939. Also, the Nazis, with their emphasis on exploitation and domination, never made adequate use of the industrial capacity of allies and subject states in Western and Central Europe. Festung Europa could have matched the industrial output of the USA and the USSR. Had the full capacity of Europe been employed in the gradual improvement and mass production of a few proven and efficient weapons systems from 1941 on (Bf-109, Fw, 190, Ju-88, etc., U-boats, Pzkw IV, shore defenses, etc), the gradual advance of Soviet forces in the East and the and if the invasion of Western Europe mght have been delayed. Couple this with the rational development of a few new designs not goverened by Hitlerian fantasies (ie, Do-335, Me-262 and Ar-234, Panther tank, Walther-engined subs) Germany might have been able to maintain both a numerical equality and qualitative edge in the type of weapons most useful in the defense of the Reich.
Of course, the Manhattan project would still give the US/UK atomic bombs by 1945. However, Europe could have been well defended, making the successful deployment of such weapons much more difficult than is was against the largely undefended Japanese home islands.