Quota system is a provison for the people coming from areas with less facilities compared to developed regions. One can't expect a student with educational background of lahore and another studying in Balochistan to have same performance. Secondly, this system assures I involvement of people from all communities and provinces to participate in national processes and education.
In some cases, this system doesn't provide opportunity to a deserving person and gives it to a person apppying on reserved seat. Unjust this may be, it ensures national harmony as well.
Civil servants may not abolish this system and instead, try to improve it by ensuring quota for every community and province according to their population only.