Why malleability is still problem in someone opinion? Through it we can change only TXID of transaction not her outputs or inputs. After some time wallet will show this transaction with new TXID. So, what a problem?
There are many problems because people do more with unconfirmed transactions then send them and wait for them to confirm before doing anything else.
For example, you may want to spend the change resulting from an unconfined transaction-- so that the rest of your coins are not held hostage until the next block-- but if the transaction ID is changed the child transactions are invalidated. You couldn't even reissue the replacement until you come back online and learn the new ID, and then imagine that the private keys are kept offline in a safe.
If you make only the most boring kinds of transactions, never deal with anything unconfirmed (including making more payments until confirmation, or replacing transactions) and use carefully and competently written wallet software then malleability is at worst a minor nuisance. If you are trying to do anything fancy with smart contracts, unconfirmed transactions (including just chaining them), or are _writing_ wallet software that has to handle malleation happening, then it's a burden and footgun.
CLTV and CSV were introduced to recover some of the worst of the damage done by malleability-- without them you couldn't safely do multiparty escrows with timeouts... but even with them the fact that malleation invalidates subsequent spends makes life hard in many ways.
You can also think of it as changing the outputs: an output is a txid, index, scriptPubkey, and an amount. The malleation doesn't change the index, pubkey, or amount... but it does change the txid of the output; and this is precisely the problem that segwit solves.