I think I can think of a good technical reason why.
Just think of how many different databases Apple must maintain that make use of your apple id. These forums, the online Apple store, the iTunes Store, iCloud, Mobile Me, Game Centre, the Mac Store, etc...
Now, each of your apple ids will have a unique identifier, and each of these databases will have a reference to it, and will probably even use it against each entiry in the database relevant to you. To merge your id's, Apple will either have to update all of these database, or provide a mechanism to allow them to map your one id to your other. Different database may also reference the unique id in different ways. They may just simply re-use it as a unique identifier for you, or they may map it to their own unique identifier. As a software developer, the thought of having to update that many databases, with those many records, is something I would really want to avoid.
It may also introduce unique key and sequencing issues. Imagine, for example a database that stores a sequence of your purchases, like this:
appleid1, 1, Heroes season 1
appleid1, 2, Lost season 1
appleid2, 1, Californication season 1
appleid2, 2, Californication season 2
Now, if they were to update that table to merge appleid1 and appleid2, you'd then have duplicate entires for appleid1 and sequence ids 1 and 2. This would likely cause a unique key violation in the database, and would also mean the true sequence of purchases was lost (now, this is a bit of a rubbish example, as it's a bad database design, but I can imagine there may be similar issues).
There could also be issues if they maintain summary tables, for example with a count of your total number of purchases, so that the count didn't need to be recalculated each time. If they were to then merge accounts, they'd need to recaculate all such values.
Then there's factors like partitioning and sharding which mean information for your different accounts may not even be on the same physical machines, which would make merging them even more difficult.
There's also the matter that any DRMed purchases you've made from the iTunes store have your AppleID embeded in them. So, they'd also have to provide a solution to this.
So, whilst I am annoyed immensley by the situation, I can also understand that it may be far from a simple problem to solve.