https://diyhpl.us/wiki/transcripts/scalingbitcoin/hong-kong/segregated-witness-and-its-impact-on-scalability/There are still malleability problems that remain, like Bitcoin selecting which part of the transaction is being signed, like the sighash flags. This remains possible, obviously. That's something that you opt-in to, though. This directly has an effect on scalability for various network payment transaction channels and systems like lightning and others
IMO, segwit is a clean up of the transaction format, but in order to do that without a hard fork, it uses a strange way of twin-block structure, which cause unnecessary complexity. Raised level of complexity typically open many new attack vectors, so far this has not been fully analyzed
And the 75% discount of witness data also change the economy of the blockchain space, so that it specially designed to benefit lightning network and other stuffs
In fact, if you do it in a hard fork, you can redesign the whole transaction format at will, no need to do so many different hacks everywhere to make old nodes unaware of the change (these nodes can work against upgraded nodes in certain cases, especially when some of the upgraded hashing power do a roll back)