If you extract chromatograms for all of the peptides in a proteome, typically fewer than 5% of those peptides will be detectable either because they are low abundance of because the peptide does not ionize well inside of a mass spectrometer.
You might want to reduce the number of peptides that you are extracting chromatograms for by only including peptides that have been detected in other experiments. Spectral libraries can help with this.

Another thing you could do to reduce the size of your extracted chromatograms would be to have some sort of retention time prediction and tell Skyline to only extract chromatograms from within X minutes of the predicted retention time (you do this in the "Retention Time Filtering" section on the "Full Scan" tab at "Settings > Transition Settings")
You can predict the retention times for all of the peptides in your document by going to:
Settings > Peptide Settings > Library
and building a library and choose "Prosit" for the "Data Source". Also you should choose something for the iRT standards that is present in your samples.

Hope this helps,
-- Nick