[Nexus 7 Q&A, Help & Troubleshooting] bftb0:
There are no methods "in the wild" to alter N7 partitioning. No doubt it could be done with "nvflash" if we had Nvidia/Asus private keys, but I wouldn't hold your breath waiting for that to happen.

Also, you could manually re-create the /system ext4 filesystem by hand (e.g. using mke2fs under TWRP) to tweak certain options to alter the ext4 overhead, but I really doubt you will gain much from doing that. You would also need to make sure that your recovery performed /system wipes thereafter using "rm -rf" instead of re-creating the ext4 filesystem... otherwise those changes wouldn't persist across ROM flashes or Nandroid restores)

I have a CM 10.2 ROM on my device right now, and "df" (terminal emulator or "adb shell df") reports 655,104 1k blocks in total file system size, with 414,168 used (63%).

OTOH, I have a KOT49H nandroid backup, and I see that the TWRP "system.ext4.win" backup file is 600+ Mb... so apparently the newest (KOT49H = 4.4.2) Factory ROM from Google is a bit of a pig.

(The TWRP archives are just tarballs, and mine are not compressed, so they *approximately* reflect disk usage when installed into a ext4 filesystem. I was too lazy to restore KOT49H to see how much actual space it would take up)

I think the suggestions you have stated are really your best options.

start taking a look in /system/app and /system/priv-app to see what is taking up all the space, and start getting rid of stuff (apps you don't use). Or perhaps move some system apps to /data/app**

Here's the "top 40" usage from KOT49H in /system:

-rw-r--r-- root/root 35440244 2013-11-28 01:27:33 lib/libchromeview.so
-rw-r--r-- root/root 25124722 2013-12-11 00:02:23 app/PlusOne.apk
-rw-r--r-- root/root 19674996 2013-12-11 00:04:06 lib/libwebviewchromium.so
-rw-r--r-- root/root 19032528 2008-08-01 05:00:00 usr/icu/icudt51l.dat
-rw-r--r-- root/root 15826119 2013-12-11 00:05:05 priv-app/Velvet.apk
-rw-r--r-- root/root 15557503 2013-12-11 00:01:39 app/LatinImeGoogle.apk
-rw-r--r-- root/root 12919557 2013-12-11 00:02:38 app/QuickOffice.apk
-rw-r--r-- root/root 12296345 2013-12-11 00:04:27 priv-app/Launcher2.apk
-rw-r--r-- root/root 11981284 2008-08-01 05:00:00 vendor/pittpatt/models/recognition/face.face.y0-y0-22-b-N.bin
-rw-r--r-- root/root 11768578 2013-12-11 00:03:11 framework/framework-res.apk
-rw-r--r-- root/root 10903908 2013-12-11 00:01:32 app/Hangouts.apk
-rw-r--r-- root/root 10714004 2013-12-11 00:03:35 lib/libearthmobile.so
-rw-r--r-- root/root 10659152 2013-07-29 23:59:34 usr/srec/en-US/rescoring_lm
-rw-r--r-- root/root 10641384 2013-12-11 00:03:44 lib/libgoogle_recognizer_jni_l.so
-rw-r--r-- root/root 10417331 2013-11-28 01:25:04 app/Chrome.apk
-rw-r--r-- root/root 9740321 2013-12-11 00:04:45 priv-app/Settings.apk
-rw-r--r-- root/root 9528752 2013-12-11 00:03:15 framework/framework.odex
-rw-r--r-- root/root 8513051 2013-12-11 00:01:02 app/GalleryGoogle.apk
-rw-r--r-- root/root 8493004 2013-12-11 00:03:23 lib/libLLVM.so
-rw-r--r-- root/root 8333828 2013-07-29 23:56:15 app/GooglePinyinIME.apk
-rw-r--r-- root/root 8111070 2013-12-11 00:04:41 priv-app/PrebuiltGmsCore.apk
-rw-r--r-- root/root 7979409 2008-08-01 05:00:00 priv-app/Wallet.apk
-rw-r--r-- root/root 7531998 2013-12-11 02:00:42 app/YouTube.apk
-rw-r--r-- root/root 7455155 2013-12-11 02:00:42 app/Maps.apk
-rw-r--r-- root/root 7383526 2013-12-11 00:01:21 app/GoogleTTS.apk
-rw-r--r-- root/root 7370099 2013-12-11 00:02:03 app/Music2.apk
-rw-r--r-- root/root 7170651 2013-12-11 00:00:55 app/Drive.apk
-rw-r--r-- root/root 6150752 2013-11-28 01:25:56 app/Magazines.apk
-rw-r--r-- root/root 6126834 2008-08-01 05:00:00 priv-app/Phonesky.apk
-rw-r--r-- root/root 6023439 2012-11-19 16:55:46 lib/libnjubase2.so
-rw-r--r-- root/root 5519762 2013-11-28 01:24:38 app/Books.apk
-rw-r--r-- root/root 5461064 2013-11-28 01:25:34 app/GoogleHindiIME.apk
-rw-r--r-- root/root 5401442 2013-11-28 01:25:10 app/Currents.apk
-rw-r--r-- root/root 4874800 2013-12-11 00:04:01 lib/libvideochat_jni.so
-rw-r--r-- root/root 4543143 2013-12-11 00:01:08 app/GoogleCamera.apk
-rw-r--r-- root/root 4529044 2012-11-19 16:55:46 fonts/DroidSansFallback.ttf
-rw-r--r-- root/root 4431628 2013-12-11 00:03:57 lib/libpatts_engine_jni_api.so
-rw-r--r-- root/root 4353896 2013-12-11 00:00:58 app/EmailGoogle.odex
-rw-r--r-- root/root 3932520 2013-12-11 00:03:47 lib/libgtalk_jni.so
-rw-r--r-- root/root 3837744 2013-12-11 00:01:19 app/GoogleEarth.apk

** YMMV. I understand that - for reasons that I don't understand - that certain Android system apps can't be installed correctly as user (/market) apps. I don't know what the details are, but it seems to me that some apps (e.g. Maps? Chrome? ) run fine well when installed on CM without the use of "gapps" installs.

If you are manually removing system apps, be sure to clean the corresponding entries from /cache/dalvik-cache, /data/data and /data/app-lib.

good luck.