I have never read any such publicly stated regret, although my study of Eisenhower focuses more on his military life before he became President.

But everything I've seen shows that for the rest of his life he maintained the same story about the post-war division of Europe-- that it wasn't up to him. Those lines were drawn by Roosevelt, Marshall, Churchill and Stalin at the Yalta and Tehran conferences, while Eisenhower stayed in the field to direct the actual military campaigns in North Africa, then Italy, then Europe.

However, even by 1948, when he published his memoir, Crusade in Europe, Eisenhower had been asked this question so many times before that he discusses at length why the capture of Berlin was not a priority for the western Allied forces. Briefly, they are:

1. Berlin is located in east Germany, and legitimately fell in the agreed-upon Soviet zone. The closest Ike came during the war to commenting on this was to push Marshall several times to insist that the Occupation Forces be set up in a Quadpartite four-power unified commission to deal with any problems or disputes. He was mostly successful in this.
2. Eisenhower pushed for, and received, permission to communicate directly with Stalin about military matters. The prevailing command culture in the US Army at that time was that commanders should be given a wide latitude to perform their tasks, and if they did not produce results, they were replaced. This was a frustrating contrast with the British system, where higher level commanders routinely expected to be micro-managed by the civilian government on the smallest matters, including troop deployment. So Ike did communicate directly with Stalin, but was very careful to confine his messages to purely military matters, because every single message was carefully scrutinized by both sides and Eisenhower was always criticized every time he sent any message to Stalin, even though all of the messages were exchanges of tactical or strategic intelligence, or the setting up of recognition signals and boundary lines for the eventual east-west meetup of forces.
3. Eisenhower personally felt that there were at least five other military goals more important than the capture of Berlin:
   1. The destruction of the Wehrmacht and SS military forces west of the Rhine before any penetration into Germany itself. He did not want to leave any troops behind him (except for the besieged channel ports which held out to the end of the war, but all of them could be invested by a single division-- the 66th).
   2. Capture of the Ruhr region to eliminate Germany's industrial capacity to wage war. Similarly, over-running the V-1 and V-2 launch sites that were terror bombing the UK.
   3. Capture of Antwerp, which Ike felt was the only port capable of fully supplying the 79 divisions he believed he needed to invade the German homeland. This took longer than expected, especially taking the Scheldt river estuary which guarded the approaches to the port.
   4. Allied generals were greatly disturbed by intelligence reports of the creation of a nation-wide Nazi terrorist network, the Werewolf Organization. They felt that the best way to avoid years of bloody occupation counter-insurgency battles was to capture the bulk of German territory in the west before this network could be fully organized. This appears to have succeeded.
   5. Similarly, Ike was concerned at the German plans to create a "National Redoubt" in southern Bavaria that would provide a haven for armed Nazi forces to harass the allies indefinitely. He considered overrunning this region a more important priority than a US/British capture of Berlin, and directed troops from Italy and Southern France to make it their number one priority. This also worked.

Normally I offer some other sources, but in this case the man you are asking about documented his thinking and decision at great length in the primary source, "Crusade in Europe." Ike was himself an accomplished writer with a historian's soul, and he goes to great length to cite numerous military cables, messages, and battle orders from that time to substantiate every decision he made. Besides being one of the better military memoirs of all time, Crusade in Europe is still in print today, both hardcopy and easily accessible digital editions, and should be available from almost any library with a history section. If you want to know what Ike was thinking and how he justified himself to the future world, he wrote it all down very clearly. I think it is rightly considered the foundational text for understanding the war in western Europe.

Finally, during the war itself, and even several years afterward, Ike felt that a closer, friendly relationship between the United States and the Soviet Union was possible. He hoped that a Cold War would not happen, and worked hard while still in uniform to maintain close ties with the Russians, even developing a personal friendship with Marshall Zhukov during the first years of the occupation. Also Eisenhower wasn't the type to second-guess himself, or to criticize the actions of his superiors who made those political decisions. He would have said he made the best decision he had at the time on the available information.

I hope that answers some of the questions on what was going on to make Eisenhower act the way he did.