The Brazilian made his debut against Santos last week, but has yet to start alongside Messi in Barca's pre-season matches.
Cruyff believes that the club could have waited a few more years before bringing in the 21-year-old.
"They are both geniuses, but first we must see how they play with each other and with the rest of the team," Cruyff told The Trade. "Two captains on a ship could bring problems.
"If the board make a decision it must be respected, but I'm just making an observation that it may have been better to wait a few years before putting them together.
"I hoped to see them together when Messi was a little older. Neymar has many qualities, but at 21 he is not fully developed yet."