Only a coule people mentioned it, but a non full flight is almost non exsistent these days (after 9/11 they had to cut back on flights due to the drop in the number of people who will fly, plus the economy where people can't afford to fly as much). They try to pack the flights full to the brim and often over book flights.
Depending how your kids are, you might want to board before everyone to get settled in. Or if they are movers and shakers, you might want to wait until the last boarding call so they have the maximum amount of walking/moving time.
Water, water and more water. Planes dehydrate adults big time, so kids will need more too. My son is still breastfeeding, and he goes into feeding frenzy mode on planes. Snacks are good if they get hungry and airlines don't really offer food too often anymore, and some airlines charge for the in-flight food/snacks.
The water will most likely cause you to have a couple trips to the bathroom. Try to get isle seats so that you won't bother the other passengers for the multiple trips. Most airlines will let you pre select your seats when you book your flights. A direct flight sounds better at first...but just remember how hard it is for adults to sit in one place for 4-6 hours. It's nearly impossible for children to remain happy for that long. It's usually best to do atleast two legs of 2-3 hours flight with a 1.5 to 3 hours layover to let them strech their legs and do whatever they need to do. It's usually good for the parents as well as they get a moment to rest a bit from wrestling their kids in a confined space.
Some people suggest benedryl to get them to sleep. If your child goes to sleep in long car rides, the chances are your kid will also sleep during the flight. Have stuff handy to entertain them anyway. And don't bring too much, cause you are the one who'll have to carry everything most of the time. Two kids, their stuff, stroller AND your things...even with your hudband there, it will be an adventure. The simpler you can keep it, the better. You'll only be able to check 4 bags for free and they'll need to be under 50 pounds each. BTW, the stroller will need to be folded up and put through the scanner at the security check point.
Not sure, but the "no liquid" policy may still be in affect when you fly. Always check your airport and airline for any funny travel tips to make sure you don't loose important stuff at the security check point. A sippee cup you can bring, but not a full sippee cup. No childrens tylenol or other over the counter liquid medicines (only perscription medicines). I think formula is okay...so breastfed babies/kids are good to go. You can get water/drinks for them from airport vendors, but then have to dump them out prior to boarding. You can get more water/drinks for them from the flight attendants.
If you are a germ-a-phob...the plane is going to be a nightmare for you. The pillows and blankets are not new each flight and lots of times not switched for washed ones...so bring your own. The carpet is pretty nasty, so I wouldn't let them sit on the floor. People have touched everything, so if you want them play with one of the magazines, you'll have to wash it off 1st. A hotel room atleast gets cleaned (maybe not to certain people's standards) each day. Plus the air isn't really "purified" as it recirculates during the flight. It's a great place for viruses/bugs to get passed around.
As much as you try to prepare, there are always situations you'll find you're not ready for. But! You could be a lucky mom and have two kids who love to fly and will be perfectly happy the whole time.
As for the hotel cribs...bring your own crib sheets. Also, a lovey that will help them feel more at home to bring some normality back into their lives is always a life saver. Keep to their routine as much as possible even with the time changes and whatnot.
I love flying with my boy and he's not yet a year old. I have lots of friends who fly atleast twice a month or more with their children since they were 1 month old and have great experiences and horrible ones...you just never know and can only hope for the best :)