Really all stems to Nintendo not investing in a larger flash harddrive. As a result, WiiWare needs to be less than 40mb to fit. They really can't fix that without booting from SD cards, but that won't happen, because some people don't have SD cards. So they are technically behind the curve so much this gen because when you can't update whole OSs due to poor online structure, you're stuck behind the curve for a long time.
I think it would do them good not to release a WiiWare version that is gimped, at least not as gimped as it would be if they force it to fit. Fans are already a bit annoyed that they are missing out on the earlier release and losing content, as is. If they choose a Retail version with a few extras, it might work better in their favor.