I give up with iTunes

Question

I have had every iPhone since the first,  I have also had every iPad, I also have a 27' iMac so I am far from a newbie,  but the current version of iTunes is nothing more than frustrating and i am at a loss.
I am posting this to the Windows one,  as the issues are across both Mac and Windows,
ITunes used to be a great experience and one of the best apps I had ever used and designed very well.  The current versions have now become the buggiest and the possibly the worst app I have ever used.
hopefully someone here has seen these issues,  and ether there is not fix as the program is just buggy or there may be a fix.
1.     New iPhone5 for the Wife.  Fully backed up her iPhone4 and then restored on that to her new iPhone5.  I cannot set it up as new because her game high scores are important to her and Apple provide no way to save scores to any app.    The restore went ok,  except every app she had ever used and deleted was installed back on to the iPhone5 and all folders were either gone or had 1 app in them and the rest scattered every where.
2. restoring a IPhone4 backup to her old iPhone4 to give to my son as he had broken his,  resulted in a similar experience,  except his restore restored all his stuff fine,  but also put all of my Wife stuff on it too now completely mixed up.
3.  Went to remove a watched movie from the iPad Mini to make room for more.   ITunes said it was done,  and showed the new extra space.   Only to find the move is still there on the iPad,  and any attempt to put a new movie on results in a not enough room error.     Then tried to remove all movies,  ITunes showed it to be done,  and 25G free.  Only to find all movies still there and same again.  Nothing I try will make it sync properly.
So I moved the entire library to another PC and also to my 27" iMac,  both with new installations of iTunes.  Both gave very similar problems with each device,  not 100% the same issues but very close.
Basically I have now found iTunes to be incapable of the job its designed for,  and I am at a total loss as to what to try next.
As a software engineer for a international company,   I am requesting Apple freeze the source code of iTunes 11 and create a 'Stable" release as we do.  No new features are placed in this build and its an optional build for our users.  Stable builds only get bug fixes and concentrate 100% on the programs basic use.  Findings and fixes in the stable then go to make the daily version more stable,  and eventually create a new stable version.
Please get back to what you used to do well because iTunes really lets the brand down and its such a shame.
Very disappointed user.
Nic W

Answer 1

I am not a single user, or even a single device.  I have 2 Macs, 2 iPads and an iPod and Apple TV and my Galaxy Note 3, My sons both have iPhones, we share one iTunes account with 3 Apple IDs.  We have no problem using home sharing and syncing  music, email, calendar, documents, photos etc, back and forth between all the devices.
Your refusal to use the cloud, (which is as fast as your wifi can process it), baffles me.  You don't PAY for it.  You have 5 GB of free storage for each Apple ID and iCloud account.  You don't have to backup to iCloud, but should be syncing with it.   It would keep your contact list current on all devices without the redundancies.  Also calendar, etc.   The cloud is not just wireless backup, it is also wireless syncing of information.     It does not store your music, movies and other iTunes purchases.
"iTunes rarely knows what it has synced which can be demonstrated on virtually any device,"
      iTunes seems to get everything right on ours.  I have no music set to sync to my business iPad, but I do have video clips and photos.  They sync just fine to the devices without any "cross contamination" or blended content. 
"Personally I think its a simple case of too many upgrades and features without maintaining a stable code base,  it certainly seems that way, unless I hear or find something else causing this"
         Again.  I don't have any problem.  Our oldest device is an iPad 2, it handled all the updates fine and still works great.
"I now have my Wifes new iPhone5 close to what it was on her 4,  but its not exact and it should have been as simple as backing it up and restoring it to a new device,  but alas that simply does NOT work."
       Well, no.  To get the new phone running with her old content, you should have backed up the old (deleting all but the one recent backup from your computer).  Then set up the new phone as - new, with the backup from her previous phone.
"Likewise transfer all new purchased then try sync it will invariably tell you not all purchases have been copied and asks to continue warning you will need to purchase again."
      This is another issue which should be resolved by iOS 8.   Any content, even FREE, if purchased with one Apple ID is forever tied to that Apple ID.  This can be a hassle because a computer can only download past purchases from One Apple ID in 90 day period.   This is where home sharing comes in handy.  Since you have 2 computer, it would be ideal.  We handle it by making any purchases directly on the computer, so we can share.  iOS 8 is adding a "family share" feature to fix this issue.
As for full clean out - It's always a good idea every now and then (Isn't that why we delete cookies at the end of a session?)  Just like a computer, residual crud stays on our devices and a full delete or format purges it.