Most rides are available to all heights, so there will be very few rides you'll miss, mostly the "mountains", Star Tours, Indy, and most of the carnival and roller coaster/thrill rides at DCA.
If you have to go with just one day, here are my thoughts. Go Monday. It will be less crowded. Unless you care about the fireworks, Fantasmic, or World of Color, in which case you'll need to go Sunday. We're locals, so we go a lot, but you'd be amazed at how much you can pack into one day. My kids are 4 and 1, so we don't do many of the "big" rides, but your older one might be able to go on the 40" rides (my oldest wasn't 40 inches until he was about 4 1/2 years old). Usually we only go from 8AM-2PM and still get a ton in. And I'm sure others will have different ideas of how to do it, but since I've got a bit of time on my hands today, here you go:
Do the park hopper. I know some people will disagree, but that way you can see highlights at both parks. Get there at rope drop in the morning and go to whichever park does not have early entry (unless you're staying at a Disney hotel, then do go to the park with early entry, but if your budget is that tight, don't stay onsite). Have snacks for your kids, too. They will be hungry and bringing your own snacks (and water) saves a lot of money. Also, before you go, try to memorize the park maps. I see a lot of people wasting their time looking for rides or attractions that are right in front of them. Oh, and eat before the park opens. Bring some McDonalds or something from your hotel with you.
If you start in
Disneyland, go to Fantasyland first. You can ride almost all of the dark rides, Dumbo, and the Teacups within about 1-2 hours. You can save Small World for later because the line is generally fairly short and it loads quickly. If your kids are excited about Autopia or anything in Tomorrowland, do that next. (My kids only really like Autopia and occasionally the Submarines, but the subs are very slow loaders so even a seemingly short line is fairly terrible. Buzz Lightyear would be the only other ride most kids like.) Take the train from Tomorrowland over to the stop in New Orleans Square. You'll see the exciting part of the train ride with the dinosaurs and Grand Canyon, but not waste too much time. You'll want to go on Pirates and Haunted Mansion, then go on over to the Pooh ride if it's something your family would be interested in. If the adults want to ride Splash Mountain, there's a single rider line that's a lot faster than the regular line. At this point, I'd switch over of DCA either before or after eating lunch (there are plenty of other attractions to see, but if you're going to see everything...). As a side note, if you go to DL after DCA, everything still applies, but fantasyland will take much longer.
At DCA, if you start there first in the morning and are not interested in riding RSR, going on any of the faster rides, or seeing the Frozen characters (assuming they are still there), I recommend going to the Toy Story ride right away. If you wait until after DL, the Toy Story ride will have a terribly long line, unfortunately, but it's worth riding if the kids can stay in line long enough. We usually skip Toy Story even though it's amazing. We do Monster's Inc., which is easily my favorite dark ride ever since they have really put a lot of detail into it (including scent). Then, we head over to Little Mermaid, which usually has one of the shortest waits in the park.
By this time, it's usually around 2 and we leave. So, I don't have much suggestion from there, but you can see how it is possible to fit a lot into one day. Just make sure to bring a stroller so your kids can rest and try to work on your own stamina if needed (my 8AM-2PM trips are usually 10-15 miles of walking). Good luck and enjoy!
