Of course, it is not possible to do this perfectly evenly spaced, and span the entire vector, so you have to make some compromise somewhere.
Here is one possibility. It will generalize to other cases:
% Some made-up data N = 1024; a = sort(rand(1,N)); b = sort(rand(1,N));
% How much to sample N_sample = 100;
% Create an (almost) uniform sample sampleIdx = round(linspace(1,N,N_sample)); a_sample = a(sampleIdx); b_sample = b(sampleIdx);
% Plot figure plot(a_sample,b_sample)
Here is the result ...