The former Three Lions striker also wonders what could have been achieved if Glenn Hoddle, the first senior England boss he worked under, had been manager for longer.
Owen was handed his debut by Hoddle as an 18-year-old before going on to win 89 caps for his country.
Across those appearances, he scored 40 goals to rank as England's sixth highest scorer of all-time.
The forward was also part of the 'Golden Generation' during the 2000s, playing alongside the likes of David Beckham, Steven Gerrard, Paul Scholes, Frank Lampard and Wayne Rooney.
Under Sven-Goran Eriksson, England reached the last eight at three consecutive major tournaments.
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However, Owen believes that a different system to the 4-4-2 England played would have unlocked the best in the options available at that time.
He told The Sunday Session: "I'll go to my grave wondering what would happen if we played a different system.
"If we had played like a 3-5-2 or something then I mean I'm convinced we would have won something, but you know Scholes, Lampard, Gerrard as a three in midfield. We used to kill them.
"We used to basically play two of them when everyone else was playing three or even four sometimes and then we always used to say they can't play together.
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"Well, no wonder they're playing against about five Spanish lads that are all running around.
"We were so old-fashioned in the way we were playing. But those three players, listen if you were playing against a top team you could bring David Beckham into the you know inside a little bit.
"If you're playing against a lesser team then play him as the right side.
"Ashley Cole is the best left-back or best wing-back in the world at the time. You know the likes of myself and Wayne Rooney up front.
"You know I think we were (the Golden Generation). There wouldn't be many put it this way that get in the team from this generation."
The Three Lions were beaten in the quarter-finals of the 2002 World Cup by Brazil before penalty defeats to Portugal in 2004 and 2006.
Owen did hint that Jordan Pickford, Jude Bellingham and Declan Rice could have made a case for a place in the Golden Generation's line-up if they were playing at the time.
However, he remains adamant that the formation was the key stumbling block rather than any missing players.
The 45-year-old continued: "I would have changed the formation. And if you look at England over the years we've been so good with playing a back three.
"I mean back to when I first remember football, let's say under Terry Venables. We had Euro 96. We played 3-5-2 in that tournament. We were brilliant. Then Glenn Hoddle took over.
"We had a really good team again playing that formation and then we went back to 4-4-2 with Sven (Goran Eriksson) and with (Fabio) Capello and managers like that we're playing very rigid 4-4-2.
"Then we've you know we've trialled a little bit in recent tournaments with the three again. I've always thought that England for some reason, we suit that."
Owen also revealed he feels Hoddle would have been the ideal manager to get the best out of the England side of the 2000s.
The Ballon d'Or winner explained: "In terms of tactics, knowledge of football I mean, I'm fortunate still to work with him on the television as you know nowadays I mean I learn something every single time I'm on TV.
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"When we get the list that says who you're on with the next week and it says Glenn Hoddle I genuinely get excited because I think I'm gonna be informed even more about a sport that I think I know most about. I mean he's incredibly tactically aware, knowledgeable.
"Of course in a tournament one bit of bad luck, one bit of something and you're out and obviously in that '98 World Cup we played against Argentina with ten men for most of the game and still went to penalties with one of the elite teams in the world at that time and we were the better side.
"We had ten men as I say, who knows where we would have got to with him."
Hoddle spent almost three years as England boss between 1996 and 1999.
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During his tenure, the Three Lions made it to the knockout stages of the 1998 World Cup in France.
However, they were agonisingly beaten on penalties by Argentina in the last 16 after David Beckham's infamous red card.