save does compression by default now which takes time as you've discovered.
The absolute fastest albeit somewhat less convenient should be using fwrite, fread as far as pure i/o speed.
fid=fopen('filename.bin','w');
fwrite(fid,var)
fid=fclose(fid);
One test here was almost a tie, however, so likely not sufficiently faster to be worth the effort.
The way to speed it up if you can afford to lose some precision would be to only use single-precision instead of double...half as many bytes to read/write. It won't be a full 2X gain because memory access will be just a tad quicker for 8-byte rather than 4-byte increments probably, but should be observeable speedup. Of course, if you need to preserve full precision this isn't an option.
