The fixture is set to take place on Monday March 16, with the Football Association unable to schedule matches for the same days as European ties.
"I think the FA are devaluing the competition a little bit by making both teams play on Saturday then Monday," he said. "Why don't they just play it [on Tuesday or Wednesday] - what are UEFA going to do?
"I love the FA Cup and everything it stands for. Bradford's run to this point has been amazing and all that romance is there but the FA choose to make both teams play on a Monday. That is the one disappointment."
Bradford have beaten Premier League outfits Chelsea and Sunderland during this season's competition, but were unable to overcome their Championship opponents on Saturday.
"You know when you come here, you're coming for a battle," added Clarke. "If you watch the game they played against Sunderland here, everything that was in that game, was there again [against Reading].
"But we showed character and determination to stand up to anything Bradford had.
"Right from the first minute you saw the challenges going in from both teams. No quarter asked, no quarter given. It was a proper cup tie, I loved it. Everyone from the first minute was at it."
Both teams hit the post in the first half before Pavel Pogrebnyak appeared to palm the ball against the right-hand upright late on, although the Russian went unpunished.
And Bradford boss Phil Parkinson was pleased with his side's second-half display.
"I thought we were the team in the ascendency in the second period," he said. "It was always going to be a mistake or one moment of quality that was going to settle the game.
"People will say Reading have done the hard work now, but we will go down to the Madejski Stadium now and the onus will be on them more to open up.
"We will go down there and try to give a really good account of ourselves once again."
