The two Perth-based clubs presented a 52-page proposal to WAFL teams and key stakeholders on Thursday morning regarding their desire to field their own sides.
The Magpies ended their seven-year VFL alignment with Williamstown for the 2008 season and has fielded their own side since.
Malthouse said the move to join Geelong as the only Victorian clubs to have stand alone sides in the VFL competition was "absolutely vital" to the development of players and maintaining a connection across the entire list.
"There's no comparison. You've got full control, we have our own coach [Tarkyn Lockyer], he's a former player here, he knows our methodologies, he sits in on our match committee, makes recommendations," he said.
"We train as we want to play and they wear the jumper so the boys the comes who come here, the 12 we picked last year, there's every probability four or five of them may not have worn a Collingwood jumper had we stayed out of our stand alone.
"West Coast and Fremantle, some of those boys get drafted, they wear a South Fremantle, East Fremantle, Swan Districts jumper and they may never wear an Eagles jumper if they don't get chosen.
"It gives them a sense of belonging and a sense of, 'I'm a Collingwood player or a West Coast player or a Fremantle player'.
"I think it's one of those essential ingredients of bringing kids through."
The motivation behind the push from the Perth clubs stems from the need for a closer involvement with players than the current WAFL situation allows.
West Coast, Fremantle, Adelaide and Port Adelaide are the only non-Victorian clubs that don't have their own reserves side, or alignments with a specific state league club.
Players from each of those AFL clubs are therefore scattered across their respective state league teams when they're not playing for their senior side.
The other non-Victoria based clubs - the Brisbane Lions, Sydney Swans, Gold Coast and Greater Western Sydney, when it enters the AFL next year - field their own reserve sides.
Malthouse said he couldn't draw a percentage on how many players had directly benefitted from the direct feeder side but that it had certainly helped them make the transition into the seniors when time came.
"When you've got a sense of belonging, then you're not getting mixed messages, not getting confused about game structures or game plans," he said.
Malthouse also said he supported the AFL's decision not to change the finals structure until at least 2013 despite next year's expansion of the competition to 18 teams.
"If you really want to see your best sides play, make them earn a spot in the top six or seven or eight out of 18. Six out of 18 would test sides," he said.
"What makes an elite sport elite is that it's very hard to make it. It's hard to get into the eight, it's hard to be part of a side that's played in a finals series, it's hard to be successful.
"That's what makes people strive more and more and more to be better.
"Mediocrity. It just kills a competition.
"If there's a negative to that, it's for the time being."
The AFL had considered expanding the final eight to nine or potentially 10 teams, and extending the season beyond 22 matches.
