If you use an automatic packer to pack custom content into your .bsp then a lot of stuff that you don't actually need will also get packed.

What I did:

I created a .lst-file defining what to pack and where, then ran that file through BSPZIP, a program that already comes with Portal 2. Here's a step by step.

1. Open a notepad and save it as nameOfMap.lst and put it in the same location as your map. You don't have to name it the same as your map but I find it makes things easier.
   
2. Write in the file what you what to pack. Here's an example:
   
   sound/vo/hi.mp3 D:\Games\Steam\SteamApps\common\Portal 2\portal2_dlc3\sound\vo\\hi.mp3 scripts/vscripts/custom_script.nut D:\Games\Steam\SteamApps\common\Portal Reloaded\portalreloaded\scripts\vscripts\custom_script.nut
   This structure is important. Each pair of lines defines one item. The first line defines where to put the file inside the .bsp. The second line defines what local path to take the file from. So above lines adds 2 files.
   
3. Open a command prompt at the location of the map and the .lst file then run:
   
   pathToBspzip.exe -addlist pathToBspFile pathToLstFile pathToPutThePackedBspFile
   Usually bspzip.exe can be found at \Steam\SteamApps\common\Portal 2\bin\bspzip.exe. Here's how it looks like for me.
   
   
   
   !As you see I enter "cmd" to get me from Powershell to Command Prompt. Powershell doesn't let me do this.

The arrivals and departures take up a lot of unnecessary space. There's ventilation and tubes that few players even see. So I just started deleting stuff.

What I did:

1. Locate for example an arrival:
   
   \SteamApps\common\Portal 2\sdk_content\maps\instances\portal_reloaded\transition\arrival\pr_arrival_future.vmf
2. Copy pr_arrival_future.vmf and rename it to something else for example pr_arrival_future_slimmed.vmf
   
3. Open the new .vmf in hammer and go nuts deleting stuff, but of course be careful about what you delete.
   
4. Save, then use this slimmed version as a functional_instance instead of the original.

I deleted everything outside of the room you are actually in and saved 3mb on the .bsp file!