gistfile1.txt

// Usecase -- 1000 accounts with different ids
// Procedure of testing. Basically a define [1000/a] records in first set, and b define [1000/b] records in second set
public static void doMagic(Integer a, Integer b) {
    Map<Id, Account> accs = new Map<Id, Account>([SELECT Id FROM Account]);
    system.debug(accs.size());
    Set<Id> account_ids = accs.keySet();
    Set<Id> set1 = new Set<id>();
    Set<Id> set2 = new Set<Id>();

    Set<Id> set1_a = new Set<id>();
    Set<Id> set2_a = new Set<Id>();
    Integer counter = 0;
    for(Id i : account_ids) {
        if (Math.mod(counter, a) == 0) {
            set1.add(i);
            set1_a.add(i);
        }
        if (Math.mod(counter , b) == 0) {
            set2.add(i);
            set2_a.add(i);
        }
        counter++;
    }

    DateTime start1 = DateTime.now();
    Set<Id> p1 = set2;
    p1.removeAll(set1);
    DateTime end1 = DateTime.now();
    System.debug('WAY1: ' + (end1.getTime() - start1.getTime()));

    DateTime start2 = DateTime.now();
        Set<Id> result = new Set<Id>();

        for (Id x : set2_a) {
            if ( !set1_a.contains(x) ) {
                result.add(x);
            }
        }

    DateTime end2 = DateTime.now();

    System.debug('WAY2: ' + (end2.getTime() - start2.getTime()));
}

//RUNS
1. Scenario 1, a = 2, b = 3
WAY1: 1
WAY2: 32
2. Scenario 2, a = 101, b = 3
WAY1: 0
WAY2: 35
3. Scenario 3, a = 2, b = 301, 
WAY1: 2
WAY2: 2