Bearing in mind that there are nine and a half tribes in Eretz Yisrael and only two and a half in Eiver ha'Yarden, why do each of them contain the same number of Arei Miklat?
Rashi and Ramban (both citing Makos, 9b): Because in Gil'ad (which was in Eiver ha'Yarden) there were a lot of murderers. 1
Ramban #1: Because Eiver ha'Yarden was an expanse of land equivalent in size to Eretz Cana'an. 2
Ramban #2: Because of the additional forty-two towns, thirty-six were in Eretz Yisrael, and six in Eiver ha'Yarden, in which case, each side had four towns per tribe. 3
Rashi: As the Pasuk in Hoshe'a, 6:8 testifies. See Sifsei Chachamim and refer to 35:14:151:1-4 and notes. See also Oznayim la'Torh DH "eis Shalosh he'Arim ... ve'eis Shalosh he'Arim", citing Nedarim, 22a - that Eiver ha'Yarden was a place where people tended to give vent to their anger and kill (which in turn, would create a lack of sensitivity towards murder which in turn, would result in more murders be'Shogeg.
In which case the towns in both areas were equally spaced from one town to the other, so the furthest that a murderer might need to run was the same in Eretz Yisrael and in Eiver ha'Yarden. This determined the distance between the towns, and not the number of people who lived there. See Ramban. See also Oznayim la'Torah DH 'es Sh'losh he'Arim Titnu ... ', who elaborates.
Ramban: Most of Menasheh lived in Eretz Yisrael - six of the eight families ? Refer to 32:33:3:1*. Two and a quarter tribes lived in Eiver ha'Yarden, and nine and three quarters in Eretz Yisrael; each side had exactly four towns per tribe! However, some tribes had more than four, and some less (Yehoshua 21:6, 7) - PF.
When were the three Arei Miklat in Eiver ha'Yarden designated?
Rashbam: Moshe designated them still in his lifetime, as the Pasuk specifically states in Va'eschanan, Devarim, 4:41.
QUESTIONS ON RASHI
Rashi writes that there were three Arei Miklat for two and a half tribes in Eiver ha'Yarden, just like for the nine and a half tribes in Eretz Yisrael, since there were many murderers in Gil'ad. But those murderers were Meizid, whereas the Arei Miklat only protects someone who murdered Shogeg?
Ramban: Some murderers schemed to make it appear accidental, so extra towns were needed to absorb both the schemers and the genuine murderers be'Shogeg. 1
Da'as Zekenim and Hadar Zekenim: Since there were many murderers be'Meizid, it often happened that there were no witnesses and Beis Din were unable to sentence them. Hashem would then bring murderers be'Shogeg without witnesses, to kill the murderers be'Meizid - in front of witnesses - who would then need to escape to an Ir Miklat. 2
Bartenura and Gur Aryeh: There were also many murderers be'Shogeg in Gilad. 3
Sifsei Chachamim: In Gilad there were many murderers who killed be'Meizid without witnesses, and who claimed to be Shogeg. 4
Ritva: Afterwards, they would discern who was Meizid, and who was Shogeg. Perhaps if there were not enough towns [nearby], it would absorb as many murderers as town residents, and it could not absorb another murderer (PF).
Refer to Sh'mos, 21:13:3:1**.
Mizrachi: This is unreasonable. Surely the number of Shogeg murderers is according to the population! Gur Aryeh ? we need not say so! People in Gilad were not so careful to avoid any chance of accidental death! (Perhaps this is because they became desensitized to murder - PF). Alternatively, the place 'raised' people who would spill blood, both Meizid and Shogeg.
This is fine if we say that one is Chayav Galus through his own admission (the Ritva in Makos 2a is unsure about this). Extra towns were needed to absorb both murderers be'Meizid and be'Shogeg. However, even if admission does not obligate Galus, presumably, if one said 'I killed be'Shogeg. Let me live in an Ir Miklat, and protect me from the Go'el ha'Dam!', we would consent, especially if it seems that the Go'el ha'Dam wants to kill him (PF).