The pair have been leading figures in the Lions' star-studded engine room in recent years, with Neale earning Brownlow Medal honours in 2020 before Lyons amassed a career-best campaign last year to claim a place in the All-Australian squad.
Headlining a dazzling pack of midfielders for the season ahead, the gun duo are set to see their time throughout each weekend shared between the centre of the field and across other lines of the ground to best suit Fagan's rotations.
With the likes of Zac Bailey and the returning Cam Rayner set to see greater minutes in midfield, Neale is set to spend more time on the wing and in attack, with Lyons also tipped to be gaining greater attention as a forward asset.
Further emerging names in Nakia Cockatoo, Hugh McCluggage and Jarrod Berry will also press their case for ascendancy in the onballer pecking order, while skipper Dayne Zorko is training at half-back as a product of Fagan's new-look midfield.
"It’s a good discussion we have been having with our midfield group – there is no doubt the likes of Jarrod Berry, (Hugh) McCluggage, Bailey, Rayner, those types of guys, (Nakia) Cockatoo as well, can play in there, and they bring different attributes," Fagan told AFL.com.au.
"Lachie and JL (Lyons), we have had chats about that, and they understand their roles will change a little bit.
"We are confident those guys can contribute in other parts of the ground as well, and the good part about that group of players is that they are all good forwards. They can all score. We just have to work out ways to use that tremendous asset we have against opposition teams.
"Lachie and JL understand. They are here to win premierships, not to win individual awards, and they know it is going to take all of us to do that, not just a few.
"JL is probably more of a forward, and Lachie is a pretty handy player out on the wing, as well as a forward, so we have a few different options there."
Lyons and Neale were the two leading ball-winners for the Lions last season, combining for over 55 possession per game.
While they will remain the first and second string midfielders under Fagan, the Lions senior coach is sure to be placing some priority toward the development of Rayner and Bailey.
Rayner is prized to return from a season-ending ACL injury that kept him off the track for the entirety of the 2021 season, with the former No.1 draft selection now entering his fifth season with the Queensland club.
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Lions fans are set to get a glimpse of how the 22-year-old has recovered in his likely return this week, with Brisbane scheduled to face Adelaide at Metricon Stadium on Friday for a pre-season hit-out.