Maybe I misunderstood you, but it sounds like you are placing three groups of data in the same drawing... plan (top), profile (side), and section (elevation).
*If* that is correct, you can reduce files size in the way you work, by placing each category in it's own separate drawing. If you need to work on one while referencing the data from another, use XREF.
Regardless of my first comment, try
vla-purgeall to reduce file size before saving the drawing.
For the best possible solution for your situation, you might want to post a sample drawing. Allowing us to see what you're working with, might reveal other suggestions.
Cheers!