I mentioned the problem with relaying tweeked transactions with different hashes in 2011
https://bitcointalk.org/?topic=8392.0We should start recommending a caconical unique tx format and make it mandatory quickly.
As to the severity of the problenm, it is cosmetic, long known, doesn't lose bitcoins, and exchanges should know better and generate their own unique transaction hashes from the transaction data.
That said, it's getting us a ton of bad press among the non-technical, and needs to be nipped in the bud.