Who was met
Targum Pseudo-Jonathan, Rashi, Rashbam, Ibn Ezra, and S'forno (on that verse) all understand that it was Moshe who was met.
However, Ibn Ezra (there) quotes an opinion that it was Moshe's son Eliezer who was met. Rabbenu Avraham ben HaRambam (there) quotes this explanation as well. Rabbenu Hananel (commentary here and to Yoma 85b as well as being quoted by Rabbenu Bahya) similarly says that his son (Eliezer) was met.
Shadal (there) suggests that Moshe's older son Gershom was the one who was met.
According to Yerushalmi Nedarim 3:9, Targum Onkelos, Pseudo-Jonathan, Ibn Ezra, Rabbenu Bahya, and S'forno he was met by an angel. According to Ibn Ezra (second commentary), Shadal and Artom, the "divine meeting" refers to a sudden illness.
Who was to be killed
Presumably the one to be killed was the same one who was met (given the repeated pronoun).
Targum Pseudo-Jonathan, Rashi, and Rabbenu Hayyim Paltiel (there) indicate that indeed it was Moshe who was to be killed. Rav Sh'muel bar Hofni Gaon (quoted in Ibn Ezra's second commentary), however, is adamant that it was Eliezer who was to be killed; not Moshe.
Who was to be circumcised
According to Targum Pseudo-Jonathan Gershom was supposed to be circumcised.
According to Rashi (4:24), Ralbag, Rabbenu Avraham ben HaRAmbam (there), and Shadal (4:25) Eliezer was supposed to be circumcised.
Reason for severity of punishment
Rabbenu Hayyim Paltiel suggests that although not circumcising on time doesn't generally carry such a severe punishment, perhaps non-Jews have a stricter punishments for not circumcising (non-Jews who are commanded in circumcision, that is). Alternatively, he suggests that the penalties were more severe since Moshe was a very righteous person, and righteous people are judged more strictly.