Green Lantern, Kingda Ka and Superman (flyer) are bunched together, and all get long lines. Go there first and try to knock out at least two of them if you get there at opening, whether you have a Flash Pass or not. Then cross over to El Toro and Bizarro. Hit the Runaway Train, then take the just-steps-away Sky Ride to the other end of the park. Nitro is there, the best steel coaster in the park, although I've heard their operations are slow recently. Batman is nearby and remains a very intense invert. Dark Knight is a P.O.S. in a box..i.e, indoor Wild Mouse. Way lame. Walk back from there to the main plaza, and you'll find a few flats and SkyScreamer, which is way better than Windseeker, IMO. Then decide if you want re-rides on coasters.
My normal strategy is to go straight to Kingda Ka (if it's running). Even at rope drop, you can expect to wait 45-60 minutes to ride because the coaster can take some time to get going in the morning. However, if you wait until later in the day, you'll be look at 2+ hours to ride the record breaking coaster.
After Kingda Ka, we typically head over to El Toro. The lines for this coaster have surprisingly subsided slightly over the past year or 2, but you can still expect to wait 30-60 minutes.
We will then typically hit Bizarro/Medussa, which is usually walk on, or at least less than 15 minutes. Then it's off to check on Green Lantern and Superman. Having riden Tatsu and Manta, Superman just isn't that great, and SFGAdv does a terrible job of expediting the loading and unloading of their flying coasters. Even with what appears to be a short line (through the first ground level switchbacks), you can sometimes wait 30-45 minutes to ride a pretty boring coaster. Same goes for Green Lantern, but they tend to do a slightly better job expediting. However, if you can hit Green Lantern before noon on a Sunday, you can probably not have to wait more than 30 minutes to ride.
We'll then head over to the south side of the park and Nitro. Since Nitro rarely breaks, and has a high capacity and 3 trains, even what appears to be a long line, moves very fast. Even after lunch, you can typically get on Nitro in less than 30 minutes. The other coasters are up to you. Dark Knight and Batman are nothing special in my book, so I will only ride them if the line is 15 minutes or less. We typically will leave around 3-4 because the crowds start showing up, and we've already ridden everything we've wanted, and more.
It really depends if this is a once in a lifetime trip and also depends on what type of rides you have in your home region. We made a trip to Cedar Point in 2004 with the explicit reason to ride Dragster, which was new that year. We built in 3 days for the trip, and were fortunate to get on a couple of times even though the coaster was down more than it was up. However, if I had known Dragster was going to be down when we had planned our trip (it was down for much of the late spring and summer while it was still testing), I made have rearranged my trip to make sure I'd have a decent chance of riding. If you feel that way about El Toro, I'd definitely wait.
If you live in Ohio, Cedar Point has a comperable match coaster to coaster with SFGAdv, except for El Toro (Mean Streak isn't even close). World-class woodies just aren't really common anymore (at least ones that are well maintained and re-rideable), so if you don't get to ride any of the top 10 very frequently (which in my book would also include Thunderbolt, Ghostrider, Raven, Cyclone, Lightning Racer, Thunderhead, and Rebel Yell), I would probably rearrange my trip to next year, when it's more likely El Toro will be running.
-You live near the park and/or visit at least once a year (or every other year)
-You've been on El Toro several times in the past
-You likely would not be able to return to the park for several years
If none of these apply and you are certain you could visit next year, you might be better off waiting. If you were going specifically for El Toro, it could be worth it to delay your trip as well. While El Toro is the park's best coaster, there are two other top tier coasters as well (Nitro and Kingda Ka), and three or four others that are worth multiple rides (Bizarro, Superman, Batman, and Green Lantern depending on preferences). It's not too difficult to fill a full day at the park without El Toro.
In short, if you really want to ride El Toro, have never been on it before, and could definitely go next year, wait. Otherwise, just go and do everything else. It's better to visit and miss one ride than not visit at all and miss everything.
I came home Friday, which was National Roller Coaster Day, to find out the news about Toro. Talk about a bad coincidence. I was invited to ACE's Running Of The Bull in a few weeks, but I dunno. They're not cancelling the event. It's also not definite it's done for the season. Likely, but not definite.
To the OP...Nitro, Ka, Bizarro, and Batman are worth the trip from Brewster if you don't get there often or haven't been.