There is some controversy actually on whether the US had to drop the bombs or not.

By that stage in the war, the US had Japan completely surrounded and cut off from supplies/oil/etc. Many people have said Japan would have surrendered in a couple of weeks anyway.

Some have speculated the real reason to drop nukes on Japan was to send a message to other countries like Russia that the US was the new "big dog".

There is also some evidence that Russia was planning to move on Japan, so the US decided to move first and decisively. Using nukes would deter the Russians. 

But you're also forgetting about US territories such as Wake Island, Guam, and the Philippines where both military and civilian populations were abused and tortured by the Japanese Imperial Army. Many people did die....slowly and painfully in many cases. As I said before, the atom bomb was the more sane approach to ending the war. I don't believe in revenge but war is war, which is why war should be avoided at all costs.

If he had testicles he would say "You guys came out of nowhere and attacked a military port without provocation, then proceeded to thoroughly FUCK Asia. You had it coming."

But if he was smart, he wouldn't go at all. Sounds like a stupid maneuver that will piss off a large group of people regardless of what he will do when he gets there.

1.  I believe that the justification given was that they were targeting a military target (naval base, military factory, etc.) that just happened to have a city full of civilians around it as collateral damage. 

2.  The alternative to shocking the Japanese into surrender with the A-bomb was to launch a full scale invasion.  Estimates suggested that there would be not only hundreds of thousands of Allied casualties, but millions of Japanese ones, mostly civilian.  I believe the population was getting close to starvation at the time.  (During the occupation after the surrender, the USA shipped in massive quantities of food.  If I remamber correctly, and I may be misremembering, the Japanese even nicknamed Americans "the rice people" for the rice they were given.)  Therefore, dropping the A-bombs counterintuitively probably saved many Japanese lives as well as American ones. 
https://en.wikipedia.org/wiki/Debate_over_the_atomic_bombings_of_Hiroshima_and_Nagasaki

3.  I don't think even the most unrealistically high estimates of Japanese casualties due to ratiation sickness etc. pump the ultimate casualty numbers up to a million. 
https://en.wikipedia.org/wiki/Atomic_bombings_of_Hiroshima_and_Nagasaki#Post-attack_casualties

Oh yeah, the Russians had every intention in moving in on Japan. The atom bombs not only brought a quick surrender but it also sent a message to the Russians to stay away. The Emperor and his advisors also feared the Russians but the extreme right-wing element of the Japanese imperial army who were encouraging citizens to fight to the death and were also trying to take over the government while holding the Emperor hostage didn't give a shit about the Russians. But again, history was on Japan's side. What happened in Germany and Korea could have easily happened in Japan. It didn't. As I said before, out of all the terrible decisions that were made, the ussage of the atom bombs were the least terrible. If anything, they saved Japan.

The US was supporting UDSSR and Great Britian in the war.

As far as what happened, I remember seeing a History Channel thing explaining that Japan wanted to surrender. When the first warning was issued, Japan said no. So no more Hiroshima.

It got tricky after that. Apparently there is a specific "No" in Japanese that is used in bartering to essentially say "I don't want those terms, but I want what you're offering". I guess sorry of a "let's negotiate this surrender" kind of thing. However, the translator just read it as no. Bomb number two drops on Nagasaki. It was at that point that Japan surrendered under our conditions.

So I believe the first bomb was necessary. It sent a message saying "We can and will end you, and anyone else who thinks they can stop us." But apparently that seconds bomb could have been avoided.

Eh an apology is fine to me. The apology would be largely meaningless for Americans anyways, as most people would think that Obama did not have anything to do with it.

While in the Japanese mindset, apologizing for others and even entire countries is very important. So it would be something largely meaningless to us but meaningful to them.

The Atomic bombs were fine at ending the war, and I am sure many people are grateful for American occupation rather then split occupation with Russia.

Yes. Everyone should apologize for their war endevours. War is fucking stupid.
I think it would be beautiful to actually apologize for something their nation has previously done.

The problem with Japan wanting to suttender is that they did not want to agree to the Potsdam declaration. Their idea was that everybody stops fighting and goes home. They way they wanted it, their government along with the radical right-wing elements of the army and within the government itself would still have been present. That would be just like the US and British accepting Heinrich Himmler's surrender offer that would have freed the Jews but also would have left the Nazi government along with institutions such as the SS intact. By 1945, too much blood had been spilled and too many people had died for everyone to simply turn around and go home.