(a) Why does Abaye answer that there are more murderers in Ever Yardin, when the commandment precedes the conquest of Eretz Yisrael itself? Abaye's answer seems to be that we place three cities there as a result of where the murderers live, but that occurs long aftere the six cities have been designated. Hash-m obviously knows where the murderers will reside in the future and thus specifies this seeming imbalance.
(b) Also, the cities of the Levites certainly squews the balance tremendously in Eretz Yisraels favor.
(a) The GUR ARYEH on the Torah (Bamidbar 35) explains that certain places are more destined to raise killers than others. He apparently is making a reference to the Gemara in Nedarim 22b which says that people are more likely to get angry and kill in Ever ha'Yarden (Gil'ad) than in Eretz Yisrael. See also Sanhedrin 24a, where the Gemara compares the calmness of Talmidei Chachamim in Eretz Yisrael to the agitation of those outside of Eretz Yisrael.
If so, there were probably more killers in Ever ha'Yarden in the times of Moshe, and it was clear that that would be the case in the future as well. (See also Beis ha'Levi Parashas No'ach, who explains who the actions of people in a particular location influence all who later enter it.)
(b) It was more expensive to live in the Arei ha'Levi'im, since they had to pay rent (13a). Not all could afford that. It is likely that even those who maintain that the Arei ha'Levi'im are free held that these cities were not as prepared to accept killers as the six cities, since we see that the Pasuk itself differentiates between them (see Aruch la'Ner there). Perhaps they had the right to reject a killer, saying that they have no more room. (In addition, the Gemara on 10a explains that the six cities protect the killer even if he entered them unintentionally.)