Personally I think the opposite is true - 99 had a much stronger starting line up, but much weaker squad depth.
After Keane, Scholes, Beckham and Giggs the only decent midfielder we had was Nicky Butt - Blomqvist and Cruyff were pretty average at best and after that it was Jonathan Greening. Right now with Valencia, Nani, Young, Giggs, Scholes, Carrick, Cleverley, Jones, Anderson, Kagawa and potentially Fletcher to come back we have twice as many good midfielders, even if none of them are of the quality of the 99 starting four.
Similarly in defence - only Vidic or Ferdinand would get into the starting line up in 99, but Berg, May and Curtis wouldn't get in the squad nowadays, and Johnsen would probably be fourth choice CB.
I think the stronger squad reflects the demands of this season versus ten or twelve years ago. More money spent by City and Chelsea means we can't afford to put everything into the first team and be left with poor quality backups who will mean we draw 13 games and lose at home to Boro. We need to have a more even balance across the team so we don't get screwed by a single injury or suspension.
That was our big Achilles heel back in those days - trophyless in 95 due to the Cantona suspension, in 98 due to Keane's injury, almost won nothing in 04 due to Rio's suspension. Our squad back then would never have pushed City so close last season with the volume of injuries we had.
