Yeah don't ever use matlab's save as "pdf", it's terrible.
Two things if you are still going to do it this way:
-When you save as .pdf, the image will be produced according to the window size of your figure
-Look at your graph's, notice how they're rugged and "jaggedy"? That's a flaw of matlab.
I know you're attaching these figures in a document so here's something you should definitely do:
Go into matlab.
Create a new script file.
Place the following commands in it:
format long
format compact
set(0, 'defaultFigurePaperType', 'A4')
set(0, 'defaultFigurePaperUnits', 'centimeters')
set(0, 'defaultFigurePaperPositionMode', 'auto')
Save the file as startup.m and save in directory:
...\Matlab\Toolbox\Local\
Now everytime Matlab starts and you produce a figure, it will scale the window and any saved file to an A4 standard where you can fit upto 2 figures on a page. (save as EPS always, and convert to pdf).