First of all, the tragedy of the deaths per se of Rabi Akiva's students is not what is being mourned during sefira. For the tragedy of their deaths pers se we have Tisha Ba'av.
Reb Aharon Kotler explains that since due to Roman persecution the number of real Torah scholars had dwindled, almost our entire tradition as a whole tradition came through Rabi Akiva. The role of these students would have been comparable to the role of the generation of the desert who received the Torah from Moshe, directly from his communication from Hashem.
Since they were to be the transmitters of the tradition, there could not be any flaw in their attitudes towards eachother, similar to our receiving the Torah at Mt. Sinai, as one man with one heart.
Their death was a tragedy in the transmission of Torah for all future generations. We lost so much and instead we received whatever we could through the few students with whom Rabi Akiva started anew.
It is appropriate to reflect on the loss of their Torah and to work on our character traits this time of year, leading from leaving Egypt to receiving the Torah on Shavuos especially since Hashem saw it fit for them to die specifically during this time period.
It is the fact that this epidemic only hit the greatest students of the generation and specifically during the days leading to Torah being given to us that our sages saw fit to mourn them and their Torah during this extended period so that we will focus on refining our character traits in preparation for that important day.
As far as the holocaust is concerned, many sages have commented on the unique level of this tragedy amongst our other national tragedies. However, it happened over the period of at least 6 years, without any specific time of year as its overall focus, so it belongs with the other tragedies.