I'm just skimming the posts here, but one point I'm surprised hasn't been raised: Any targeting plans regarding Germany would have been considerably shaped by the more robust aerial defenses the Reich still possessed at the end of 1944 - defenses much more robust than those of Japan in August 1945 (which were negligible at best, with the remaining planes, fuel and pilots being hoarded for use against OLYMPIC and CORONET).
In fact, there wasn't much planning at all with regards to targets in Germany. In part this was because of the prospect that the Bomb would not be ready in time anyway, but also because of concerns over the dangers that a bomber would be shot down, and the risk the Germans might recover it intact. The first targeting discussion, in early 1943 (involving a group composed of Gen. Groves, Vannevar Bush, James B. Conant, Admiral William Purnell, and Major General Wilhelm Styer) actually proposed Truk Lagoon, which at that point was the main base for the IJN Combined Fleet:
More directly interesting is a postwar interview with Leslie Groves, where he digs into the dangers of German aerial defenses:
Working from this discussion, I think that if Groves had been ordered to bomb Germany at the end of 1944, what you would need to do would be this:
1) Proceed to deploy a sizable number of squadrons equipped with B-29s to England in 1944 as soon as they became available (which would of course impinge on deployments to Guam), and work them into bombing raids over a variety of German targets during daylight;
2) Efforts would be escalated to wear down Luftwaffe fighter defenses and radar sites in western Germany;
3) The target would be a a) city still substantially intact (in order to assess effectiveness of the bomb, and also to gain maximum value from it), b) within fighter escort range, and c) no deeper into German aerial defenses than necessary.
To me, the most obvious fits would be one of the German coastal cities on the North Sea or Kiel canal. Of course, most were pretty well bombed conventionally by that point. RAF and USAAF commanders might be ordered to ease up on the primary city in the months before the attack, perhaps.
4) On the raid itself, maximize protection of the bomber with heavy fighter attacks to tie up Luftwaffe assets; heavy bombing raids on other cities; and accompany the bomber itself with a sizable force of other B-29's and fighter escort.
Of course, employing a large escort means you put other planes and crews at risk for damage from the blast. There is just no getting around the fact that dropping a bomb on Germany would have been a more difficult task than doing it over Japan.
In fact, there wasn't much planning at all with regards to targets in Germany. In part this was because of the prospect that the Bomb would not be ready in time anyway, but also because of concerns over the dangers that a bomber would be shot down, and the risk the Germans might recover it intact. The first targeting discussion, in early 1943 (involving a group composed of Gen. Groves, Vannevar Bush, James B. Conant, Admiral William Purnell, and Major General Wilhelm Styer) actually proposed Truk Lagoon, which at that point was the main base for the IJN Combined Fleet:
The point of use of the first bomb was discussed and the general view appeared to be that its best point of use would be on a Japanese fleet concentration in the Harbor of Truk. General Styer suggested Tokio but it was pointed out that the bomb should be used where, if it failed to go off, it would land in water of sufficient depth to prevent easy salvage. The Japanese were selected as they would not be so apt to secure knowledge from it as would the Germans.
More directly interesting is a postwar interview with Leslie Groves, where he digs into the dangers of German aerial defenses:
REPORTER: General Groves, could we go back for a minute. You mentioned in your book [Now it Can Be Told] that just before the Yalta Conference that President Roosevelt said if we had bombs before the European war was over he would like to drop them on Germany.3 Would you discuss this?
GROVES: At the conference that Secretary Stimson and myself had with President Roosevelt shortly before his departure, I believe it was December 30th or 31st of 1944, President Roosevelt was quite disturbed over the Battle of the Bulge and he asked me at that time whether I could bomb Germany as well as Japan. The plan had always been to bomb Japan because we thought the war in Germany was pretty apt to be over in the first place and in the second place the Japanese building construction was much more easily damaged by a bomb of this character than that in Germany. I urged President Roosevelt that it would be very difficult for various reasons.
The main one was that the Germans had quite strong aerial defense. They made a practice, as every nation does, that when a new plane came into the combat area, that they would run any risk that they could to bring such a plane down so that they could examine it and see what new ideas had come in so that they could make improvements and also would know the characteristics of the plane so that they could prepare a better defense against it. We had no B-29’s in Europe. If we had sent over a small squadron or group as we did against Japan of this type, everyone of them would have been brought down on the first trip to Germany. If they hadn’t been, it would have been through no lack of effort on the part of the Germans.
The alternative would be to bring a large number of B-29’s over to to England and that would have been a major logistical task and the other possibility would have been to have used a British plane which would not have been a bit pleasing to General Arnold and also would have created a great many difficulties for our general operation because then it would be an Allied operation with the United States furnishing the bombs and everything connected with it but using a British plane and a British crew to actually drop the bomb and it would have raised a tremendous number of difficulties.
And difficulties like that — while you say you should be able to handle that — you can but in a project of this character there are so many little things, each one of them key, that you can’t afford to throw any more sand into the wheels that you can help.
The bombing of Germany with atomic bombs was, I would say, never seriously considered to the extent of making definite plans but on this occasion I told the President, Mr. Roosevelt, why it would be very unfortunate from my standpoint, I added that of course if the President — if the war demanded it and the President so desired, we would bomb Germany and I was so certain personally that the war in Europe would be over before we would be ready that you might say I didn’t give it too much consideration.
Working from this discussion, I think that if Groves had been ordered to bomb Germany at the end of 1944, what you would need to do would be this:
1) Proceed to deploy a sizable number of squadrons equipped with B-29s to England in 1944 as soon as they became available (which would of course impinge on deployments to Guam), and work them into bombing raids over a variety of German targets during daylight;
2) Efforts would be escalated to wear down Luftwaffe fighter defenses and radar sites in western Germany;
3) The target would be a a) city still substantially intact (in order to assess effectiveness of the bomb, and also to gain maximum value from it), b) within fighter escort range, and c) no deeper into German aerial defenses than necessary.
To me, the most obvious fits would be one of the German coastal cities on the North Sea or Kiel canal. Of course, most were pretty well bombed conventionally by that point. RAF and USAAF commanders might be ordered to ease up on the primary city in the months before the attack, perhaps.
4) On the raid itself, maximize protection of the bomber with heavy fighter attacks to tie up Luftwaffe assets; heavy bombing raids on other cities; and accompany the bomber itself with a sizable force of other B-29's and fighter escort.
Of course, employing a large escort means you put other planes and crews at risk for damage from the blast. There is just no getting around the fact that dropping a bomb on Germany would have been a more difficult task than doing it over Japan.