What was Hashem's quandary? What does "b'Shagam Hu Basar" mean?
Rashi and Rashbam: Hashem in His Mercy, was wavering as to whether to destroy them or not - even though they were worthy of destruction, and especially since, despite the fact that they are mere flesh, they refused to humble themselves before Hashem. (Imagine if they had been fire or some hard substance!)
Seforno: On the one hand, seeing as they were made in Hashem's Image, they deserved to be wiped out; on the other, they needed Hashem's Mercy, seeing as they were also flesh, which made them prone to sin.
Targum Yonasan: The quandary refers, not to the generation of the Flood, but to future generations, whom Hashem now promised that He will not judge in the same way as He judged the current one. He bestowed upon man His Holy Spirit in order that he should do good, but he perpetrated evil, since he is flesh.
Da'as Zekenim : This alludes to Moshe. Its Gematriya is like that of Moshe (345, and he lived 120 years). 3
Lev Eliyahu (Bereishis p.33): They should have activated the Neshamah to conquer the body. They did oppositely. My Ru'ach will not remain in him, because he became physical, and not spiritual.
Rosh: "L'Olam" means a long time. Man was living so long that his intellectual soul from above was being drawn after the lust of his flesh.
"For Hashem made man straight", to be like the angels, by means of the Neshamah with which He endowed him, but he was drawn after his flesh.
Chasam Sofer (Chulin 139b) - Moshe was Reishis; like Terumah is one part in 50, so his years were one part in 50 of the world. He pertained to the 4000 years of Torah and Yemos ha'Mashi'ach, but not to the first 2000 years of Tohu, so he should have lived only to 80. However, since he was Basar (born to a woman), he was given the 80 years after the age of Binah, i.e. 40. I heard in the name of the Gra that Hashem wanted Moshe to live like a generous Terumah of the world, (one part in 40 of 6000 years). B'Shagam Hu Basar - because he asked "can You give meat for this entire nation?!", I will make him average Terumah, one part in 50, i.e. 120 years.
What is the significance of the hundred and twenty years wait until the Flood?
The hundred and twenty years were a chance for the people to do Teshuvah and be saved from extinction.
From the birth of Yefes (mentioned a few Pesukim earlier) until the Flood was only a hundred years (and not a hundred and twenty)?
Rashi: The decree of the Flood took place twenty years prior to Yefes' birth. 1
In which case, we must say that the current Pasuk was said before the Pasuk that announces the birth of Yefes (see Bereishis 5:32), in keeping with the principle that the Torah does not always follow a chronological order (Refer to 6:4:1:1). Moshav Zekenim asks that within one matter, the Torah follows chronological order! Riva answers that the Torah treats this like two matters, for there is a reason to write out of order, lest people criticize No'ach for fathering children destined to perish in the flood.
What is "Lo Yadun Ruchi va'Adam"?
Da'as Zekenim #1: When his soul rises above, I will not return it to him.
Da'as Zekenim #2: I will not create Nefesh for man.
Da'as Zekenim #3: My spirit will not dwell in man until [Moshe] will come, who has a heart of flesh.
רש"י: לא יתרעם ויריב רוחי: כאן פירש "ידון" מלשון ריב ומדון, אך רש"י ממשיך "הנה רוחי נדון בקרבי אם להשחית" משמע ש"ידון" מלשון דין?
גור אריה: גם 'נדון' מלשון ריב ומדון, כי כאשר הדבר מסופק ואין בו הכרע נקרא 'מדון' מפני שאינו שוקט.
רש"י: לעולם- לאורך ימים: למה לא פירש רש"י כפשוטו שלא ימשך המדון הזה לעולם?
גור אריה: [משמעות הפסוק שאם לא אענישם הרי ש'ידון רוחי לעולם',] ואם 'לעולם' הוראתו כפשוטו, מנין לומר שלעולם לא יענשו? אלא 'לעולם' הוראתו 'לאורך ימים' ולכן מניעת העונש היא בבחינת 'ידון רוחי לעולם'.
רש"י: שגם זאת בו שהוא בשר: משמע שהקב"ה הקפיד על כל מין הבשר ולא רק על הפרטים, וכן אמר ה' "אמחה את האדם" וקשה א"כ למה ניצלו שנים מכל מין ע"י נח?
רא"ם: אולי לא הייתה תביעה על המין בכללותו אלא על הפרטים, וכל הפרטים (חוץ מנח ובניו) השחיתו את דרכם.
גור אריה: אמנם רצה הקב"ה לבטל את המין, אבל מכיון שהיו בתיבה רק שנים מכל מין והם נאסרו שם בפריה ורביה, נחשב הדבר שנמחה אותו מין, וכשיצאו מהתיבה קיבלו על עצמם להדבק רק במינם ונחשב שנבראו אז מחדש.