Backed up iPhone BUT iTunes did not copy all my apps!

My gosh, iTunes must be one of the most frustrating tools in the world.
From the screen area that states: Manually Back Up and Restore, I select Back Up Now.... this process oddly only needs about 1 minute to backup my iPhone (with about 160 apps on it).
When I look at the app list, there are still many apps missing, such as:
Any.Do (great to-do list app)
All my Synology Apps (for my SAN device)
etc.
BTW, why the heck isn't there an option to see the apps in folders - simulate the placement and folders of the iPhone?
Underneath this back up option is a Sync option... I tried this and it did something but I am unsearch what! All I know is that it did not help!
Never mind all that above... seriously, all I want to do is duplicate all my contents from my iPhone 4 to my new iPhone 5. This should not be rocket science!
I think it should be an major embarrassment that something I can do between two Samsung Android phones is so friggen complicated between to iPhones! Yes, I have complained to Apple (this is my second iPhone trade-up) and never heard back from them the first time. That first time, I just ended up starting over! Grrr...
Anyway, enough rant.
I've gone to this page: http://support.apple.com/kb/ht2109
...and selected, "Using iTunes to transfer information from your current iOS device to a new one"
Naturally, if I cannot successfully get past step 2, this isn't going to work.
Questions:
1. Can anyone please explain why I cannot backup all my apps and tell me how to fix this problem?
2. Can anyone suggest a better 3rd party backup and restore tool (for any price!)? I am sick of waiting for Apple's Windows iTune team to fix this inept tool!         I don't mean to fight... but seriously, either this team has no budget or they are clueless to its serious shortcomings.
Sorry, I am just a little bit annoyed and expected better from Apple.

Sorry this solution is late but I just got off of the phone with Apple support and this worked. 
Open iTunes
Connect your iPhone and keep it connected during this entire process.
In the iTunes menu at the very top (File, Edit, View) choose STORE> Sign in and sign into your iTunes account.
Once this is complete look at the upper right corner of iTunes and you will see an iPhone and Store button, cick STORE.  Now you will be in the iTunes store where you see the advertisements of the various albums, songs etc.  Look on your upper left of the window for your itunes account name and in the black band next to your iTunes account name, you will see a House icon, then Music, Movies, TV Shows etc.
Make sure the HOUSE icon is selected.
Stay on this screen in iTunes and on the lower RIGHT, you will see an area that says- QUICK LINKS.  In that area click - Purchased
After you do this you will be transported to another area of iTunes.  Here there will be a menu across the top- Music, Movies, TV Shows, Apps, Books are the choices. 
Choose APPS and you will see the apps that you have purchased.  You will also see the apps that didn't download to your phone. 
Find the apps that didn't download and click the cloud next to their name.  Doing this will download the chosen apps to the computer you are on. 
Once you have downloaded the apps in question, in the upper right corner click LIBRARY.
Now you should see the button that says iPhone because your phone is still plugged in.  Click the iPhone button and then click SYNC on the lower right to sync your iPhone.  
The apps you downloaded will now be on your phone.
Sorry for the long instructions but this is what works.

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