Migration Assistant and user permissions broken

I just used Migration Assistant to my old early 2008 unibody 15" MBP to import stuff to my brand new 15" quad core i7. The old machine was connected through FW800 in target disk mode.
Somehow this process failed and it left me to an odd result which I cannot figure out how or why such things would happen. I have used migration assistant often successfully, if not exactly this way.
I already decided to start things from scratch, but I would appreciate any insight that somebody might have. Like what just happened? Do you have similar experiences?
The process:
- In my old machine I had two users, for the sake of argument, "MainUser" and "OldUser".
- In my new machine I had two users made right after a clean install, "Admin" and "MainUser". I usually work with "MainUser" so I made one without thinking about it much.
- I connected the old machine in Target Disk mode and started Migration Assistant under Admin of the new machine. First question I answered to migrate from another disk, as the other machine was in Target Disk mode. Next one asked to pick the disk and that is followed by a selection "What to migrate". I wanted to install applications from scratch, so I checked everything except applications. I do not know if this is relevant, but I would imagine it is not.
- A pop-up appeared, which correctly told that there already is MainUser on the new machine. The dialog gave me three options: 1. Rename the account that I am transferring, two with the same name could not exist 2. Replace the existing account with the one I am transferring 3. Do not transfer this account.
- I chose 2, because there was nothing worth saving in the MainUser account on the new machine. Continue.
- Watch a few hours of progress bar
- After the migration process the machine was in very odd state. I logged in as MainUser and it oddly looked like default Snow Leopard state, not like the desktop of the migrated account. No folder items that I had on the desktop previously were visible, language was default English and desktop background was the Snow Leopard nebula. I tried, but could not change that in the system preferences.
- Closer inspection revealed that I did not have permissions to access any of the folders under my username, like Documents, Music, Movies etc. This also explained the desktop problems. It meant that none of the programs were allowed to read or write any data under Library folder so everything was and stayed as default. For instance, any settings that I tried to change and which might even apparently change, would reset back on logout. Programs settings were empty, like no bookmarks on Safari or Apple Mail did not show the mail accounts.
- I checked with Terminal what was on with permissions, and for some odd reason, all the folder owners under MainUser belonged to OldUser(!).
- There is no reason that I can think of why that user account would have anything to do with this migration -- after all, the whole deal was supposed to be to migrate (or overwrite) MainUser, not to mess with OldUser in any way, except bring that over as a separate item.
- For the sake of argument, I also logged to OldUser account and that seemed to be transferred correctly. No issues with file permissions or the desktop. Only MainUser was messed.
- I decided to take the ownership of all files under MainUser account back. I did "sudo chmod -R MainUser *" to grab everything. Immediately the stuff on desktop appeared. After logout and login rest of things seemed to return (mostly) to those places that the migrated MainUser should have had, like the desktop background, dock position and even Apple Mail now showed my old emails.
Even if I sort of fixed things, I have iffy feeling about the whole process.
I decided to start over. This time I will not have MainUser account on the new machine to avoid any further hassle. While I suggest everyone to avoid this situation and not to have users with same name or let Migration Assistant to run this overwrite -option, I would like to hear any speculation why or how this might have happened.
If Apple is listening, you might check the latest Migration Assistant in the above case. There might be a bug. Thank you for listening.

I think it is inadvisable to have the same user account on the target machine when using Migration Assistant - just from recollection this is known to cause problems.
However, in my experience (and I have used MA many times across many machines), even when apparently completing successfully, MA simply does not work properly when it comes to permissions.
For example, after using MA to import my previous user account to my new MBP 2.3 i7, I cannot drag anything out of the dock - it just doesn't work.
Also, content of my desktop folder does NOT display on the desktop itself.
I have tried applying specific permissions to this folder, for my user account AND "Everyone" - it makes no difference.
I do not regard Migration Assistant as fit for purpose.

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