This tutorial can also be used as a guide to adding similar effects to multiple textures at once, such as darkening or recoloring.
One way I've found I've been able to reduce filesize through images without losing quality of any pngs is by using this method:
If you've got a lot of images, you'll want to do this all at once. If not, ignore the bits about actions and batch.
1. First, right click your texture data in brawlbox and hit export all. This will export all of the textures in that texture data. Save them to your desired location.
2. Now open one of the images you just exported (or any image, it doesn't matter) in photoshop. I have CS5, but as far as I know, you can do this with any build. Hit "window" on the top bar and check actions. Once the actions window is opened, hit the new action icon at the bottom (looks like a page). Name your new action something like "save for web."
3. Hit record. You'll see a red circle highlighted at the bottom of the actions window. Now in photoshop, go to file> save for web and devices. At the top right you'll see file type. Set to PNG-24. There is a PNG8, I assume that this reduces filesize and quality more than 24 will. There are also other options there that can further reduce filesize. Save the texture to a new folder.
4. Hit the stop button on the actions menu. You'll now see all the actions (sans the new folder) listed under whatever you named the action. Now you can easily do this action to multiple folders at a time. Hit folder>automate>batch. At the top make sure the action you just made is selected. Under source choose folder then select the folder you exported from brawlbox. Under destination choose folder and select the the folder you exported the previous texture to. Under file naming, keep it at "document name" + "extension."
5. Hit ok at the top right of the window. you'll see photoshop opening and closing all of the textures. After its finished, you can go back into brawlbox, right click the texture data, and hit replace all. Choose your destination folder that all your new textures are in. Be warned, I've had problems with the replace all feature in the past. If brawlbox gives you an error, you'll have to manually replace the textures one by one.
Now save your work in brawlbox. Using this method, as well as lowering MIP levels in brawlbox while manually replacing textures, I managed to get a 3.829 mb .pac file down to a 3.379 mb file without losing much quality, and if you wanted to, you could record further actions such as posterization to lower the file size even more.