"I watched that game closely on the weekend and he just ran the show. With Cleary out he's stepped up again and taken that role upon him and is doing a good job. We do miss him."
Regardless, Flanagan maintained the Sharks had little choice but to release Maloney as part of the swap with Moylan last year with a season still to run on his contract.
Maloney, who is the only half in history to take three separate sides to grand finals, pushed long and hard for a contract upgrade and extension at Cronulla.
"I had a side after the 2016 grand final and I'm sure they all wanted a pay rise but we just couldn't do it and that's what the salary cap does to teams," Flanagan said.
Moylan, meanwhile, has struggled to fit in at Cronulla.
Having missed two weeks through injury, Moylan's four games to start the season have been split between five-eighth and fullback.
The Sharks' attack looked far better with Moylan in the No.1 jersey and Trent Hodkinson at No.6 against St George Illawarra on Friday night, although Moylan endured a tough night in defence.
But Flanagan indicated Josh Dugan – one of three men to have played fullback this year – could move back to the custodian role once he fully recovers from a groin injury.
"What position is best for them you will probably see in the next week or two," Flanagan said.
"The best place for [Dugan] on the weekend was right centre, he's had a groin injury and we wanted to take the running load away from him … but that could change in the weeks to come."
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