I've noticed that the ATC in FS9 likes to give really low altitude intercepts for the glideslope, ie., 2000 feet or less AGL, and this is when you're in a jet too.How does the ATC in FS9 determine what altitude you should maintain till established on the loc and coming down the glide path?Why is it typically so low?

Because most approaches have a final segment about 5 miles long and that means an aircraft should be somewhere 1500-2000 above the ground at the glideslope intercept point. If you look at a typical ILS chart, you'll find that the final altitude that the MSFS ATC assigns you is close to what the charts show for crossing the FAF.

Yes, but when a chart shows 3400 feet and you're told to hold 2000 feet....

Keyword "typical".