The current system of the Wii Shop has your points stored to your Wii, not the server, so making the points universal would require completely changing the way they do things on the Wii.
They're not stored on your Wii. Well, the Wii may keep a cached value of what you have to spend, but Nintendo has your Wii internal key stored with the number of points you purchased. You also have an option to tie a "My Nintendo" account to that key.
The only thing that would be stopping them from making it more universal, is putting the emphasis on the "My Nintendo" account and
forcing you to have one. Right now it's an option.
In other words, right now you have a bunch of (Wii Key)=>(Points) records... and Nintendo plans on continuing the trend with the DSi by having (DSi Key)=>(Points) records. To make it universal, they would need a (My Nintendo)=>(Points) relation. With the current fact that My Nintendo is optional, it would be difficult of them to migrate the info... as they would have to have something in place to support the old style. Not impossible, but not easy. It may even be by choice (that they still don't want to require the "my nintendo" account). Why not, like I said they benefit from the left over points and the whole reason the DSi exists is because they saw the $$ the VC pulled in on the Wii.