Hampton, Leiter, Reed, Jones, Rusch.  1 through 3 would be the ace on the current team.  

2000 ERA+:
Hampton 139
Leiter 136
Reed 106
Rusch 109
Jones 86
Entire staff 105

2007 ERA+ (up to yesterday):
Glavine 98
Maine 117
Perez 121
Duque 134
(fifth starters: Sosa 102, Pelfrey 71, Lawrence 102)
Entire staff 105

Stats for easy reference: 2000 2007

This looks almost like a push to me, though not quite, and you're definitely overrating Rick Reed.  The 2007 Mets have a deep rotation front-to-back, and have been surprisingly good overall.

About the hitters, I'm not going to bother producing numbers, I'm just going to say that anyone seriously wishing for the return of Zeile and Payton as middle-of-the-lineup "power" hitters, to say nothing of Joe McEwing (whose best baseball skill is likeability), rather than what we've got now, has got to lend me their rose-colored nostalgia glasses so that I can write a bestselling memoir about the happy qualities of the Reagan era and the realistic graphics of the Commodore 64.

perhaps i do have rose colored glasses ... 2000 was a great year and in the midst of this up and down year ... easy to underrate 2007.
however, re the pitching staff (and i agree i overrate reed) the one-two combo at the top is clearly superior.  i admit i am surprised at the strength of this year's numbers.  things have been dicey of late and perhaps that influenced me.  curious to see where the #'s will end up.
as for middle of the order ... as i said i think our lineup top to bottom in 2007 is better.   with the exception of beltran (i should have left him out), the slugging and ops numbers in 2000 were in fact a bit better ... when you compare zeile and ventura (and payton) to delgado and green.  admittedly, ventura did not have the kind of year in 2000 than he did in 1999.
as for the bench, without endy, what DO we have now?  david newhan?  i'll take superjoe over him as a last roster spot every day of the week.
and as ridiculous as it may sound, i am nostalgic for ole ronnie ... but ONLY when i think about the disaster who holds the office now.  

I miss Bobby Valentine.  You'd never see Willie in a fake mustache and glasses, and that disappoints me a little bit.

In the midst of their best month of the season the 2000 Mets were 72 and 49 after a 121 games;the 2007 Mets currently find themselves at 68 and 53 after 121 games (that's 4 games back for the mathematically challenged).  The 2000 Mets followed their strong play in August with a lackluster September thereby losing the chance to win the division; they finished with 94 wins and .580 winning percentage.  The Mets currently have a .560  winning percentage.  The 2000 Mets finished with an actual record that was better than their Pythagoreon record.  The same holds for the 2007 Mets after 121 games.

Both teams were pretty uneven during the course of the year.  See month by month break down for 2000.  

http://www.baseball-reference.com/teams/NYM/2000_sched.shtml

Although I do not think that in game managerial decsions have a huge impact on wins and losses, I think that you would have to give the nood to Valentine in that area.

Without looking at the numbers, I think that the  current lineup is better at every position other than 2nd and catcher (note howver, that the performances of Piazza and Alfonso were far above league avergae for their positions).  

Also note that Melvin Mora was shipped off to Baltimore for Mike Bordiick and therefore probably should not be counted as a bench player for the 2000 team (Incidentally, that turned out to be a shitty trade that doesn't get much attention).

2000 bullpen was bettter, but as Anonymous demonstrates the starting staffs were pretty even.

If these two teams were to play each other 100 times, I think that it would be pretty close to 50/50.