The Magpies have made it clear that they want to scour the fields on Tyneside, searching for homegrown players.
But at the moment, youngsters who are signed up with United can't star for clubs like Wallsend Boys Club at the same time.
Thompson feels that decimates young players' game-time and also denies them the chance of extra development at places like Wallsend, the club that delivered Alan Shearer, Michael Carrick, Lee Clark, Steve Watson, Peter Beardsley, Steve Bruce, Robbie Elliott, Fraser Forster and Brian Laws to name but a few.
Thompson, who also played a big part in Newcastle's Academy and reserve team during two years at the club, told the Evening Chronicle: "You want it to go on, but it is different to when I was young.
"You could go to Newcastle United centre of excellence and still play for the boys club - now it is a bit different.
"Some people choose to join the local pro clubs and some people to still play for the boys club.
"In my opinion you should be able to do both.
"That seems to have changed over the years.
"Whether it is for the good of the game or not, I don't know."
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