Some flu patients who became ill over the winter could take up to 18 months to make a full recovery.
Across the UK, there were 569 flu-related deaths - at least 34 in Wales.
Many of the patients treated in intensive care are only now starting to recover, and need long-term rehabilitation.
Doctors say they are worried that vaccination rates among some vulnerable groups were particularly low.
One victim, Julian Skinner from Cardiff, was admitted to hospital on Christmas Day with swine flu.
"I only remember flashes really," he recalled.
"Like little still images in my memory of people around me and being told that I was going to be put under.
"I vaguely remember the ambulance ride and being carried down the stairs."
Having initially only suffered from mild symptoms, Julian's health had deteriorated rapidly because of low oxygen levels.
During the seven weeks that he was unconscious, his family were warned they could lose him.
"They were beside themselves with worry - it has been traumatic for them as well," he said.
"The first couple of weeks I was awake I had a lot of difficulty coming to terms with what happened and getting my head around it - trying to work out what was real."
Dr George Findlay, an intensive care consultant at the hospital, said they had been through a particularly busy winter.
"This year we had a particular problem with the 30-40 year old age group," he explained.
"We had a number of previously fit and healthy patients who presented with flu and got very, very ill - some of them stayed in the intensive care unit for several months."
Dr Findlay is particularly worried that some of the patients he has treated had declined the offer of vaccination.
"We had a particular problem in the intensive care unit with pregnant mums," he added.
"As a consequence we had several patients critically ill in intensive care when we could have avoided that."
The question of how to improve vaccine take up will have to be tackled before next winter - by which time Julian Skinner hopes to be back living at home.
But even after discharge from hospital, he may need up to another 12 months of rehabilitation.
"I've got to count my blessings," he reflected.
"I do feel fortunate to be alive. I'm going to try and live my life to the fullest form this point on - its shown me more than anything that you literally don't know what's around the corner."