The AFL confirmed on Wednesday it is pushing ahead with the moves that will affect father-son prospects and all academy (northern and next generation) selections.
Clubs such as Carlton and Port Adelaide, which will be impacted the most at this year's draft, lobbied hard for changes to be delayed until at least 2027.
Blues president Rob Priestley said "certain clubs will be disadvantaged more than others", while Port counterpart David Koch was "furious" and argued for gradual change.
"It's putting the V back into AFL," Koch told FiveAA Radio.
Swann believed there was a "never a good time" to introduce the changes.
"There's always someone's that got a dog in the fight. They won't all be happy," he said.
"This change got raised at the CEOs' conference in July last year, so it's a bit disingenuous to say they didn't know it was coming.
"The detail, they didn't know what was coming, but it was flagged that there was going to be a change."
Asked about the changes, Western Bulldogs coach Luke Beveridge embarked on a three-minute take-down of the AFL to conclude his pre-game press conference.
Beveridge said the AFL was a "punching bag", also referencing confusion around the ARC (AFL review centre) and umpiring.
"We're trying to make things perfect in a game that is chaotic," Beveridge said on Wednesday.
"It's not this regime's fault, it's the operational regime of the last 15 years that keep changing things.
"We're making a change on the run.
"There's some bigger challenges ahead for 'City Hall' (AFL)."
Under the old system, clubs could stockpile numerous late picks to secure a highly-rated youngster high in the draft.
But the new rules mean a maximum of two picks can be used to match a bid placed on a father-son or academy prospect.
Clubs whose first-round pick slides back due to a matched bid will also receive an extra second-round compensation selection.
Teams that reach the grand final will have a 20 per cent points loading added to their bids, making it harder for the likes of the Brisbane Lions.
Rivals were left fuming after the reigning premiers secured talented local prospect Daniel Annable with pick six in the draft, weeks after winning back-to-back flags.
That came after already recruiting star brothers Will and Levi Ashcroft under the father-son rule.
Clubs that finish from 11th to 18th on the ladder will receive a 10 per cent discount applied to bids from picks one to 36.
"The choice is you make a decision on trading a good player to get the picks, or you pass on the kid because you can't get it done," Swann said.
"We just don't want to see really good players going for 30, 33, 34, 36, 40, 42; it does everyone's head in.
"It's no coincidence it's taken to late April to come up with it because there's been a lot of lobbying."
Highly touted pair Cody Walker (Carlton, father-son) and Dougie Cochrane (Port, Next Generation Academy) could be the top two picks in this year's draft, meaning the Blues and Power will have to pay more than they would have previously.
The Power also have further eligible talent coming in 2027 with Louis Salopek (father-son) and Zemes Pilot (NGA).
St Kilda have been the club most vocal about wanting change, targeting the Queensland teams for their access to academy talent.
"They're happier," Swann said of the Saints' response to the changes.
"I don't know if you could call them happy because they want it harder.
"Just some of these clubs have been down for too long."
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