You might want to read DLR29's "Magic Morning Superthread" which talks about strategies for your MMs.
http://www.disboards.com/showthread.php?t=1675403&page=5 This takes you to page 5, which has some posts at the bottom and on page 6 about Nemo specifically.
Nemo is open for MM. (Space Mt. and Buzz are, usually, too.) It's still very popular, and many, if not most, of the people in line for MM are stampeding directly for Nemo (thus the expression, "the Nemo stampede").
When we did it in March, we got to security at 6:10 a.m. for a 7 a.m. MM. We were third in line. When security opened at 6:30, we hurried to the turnstiles and were first in line at our turnstile. They opened the turnstiles at 6:50 a.m. (by which time the lines were back farther than the middle of the Esplanade), and everybody went up to the top of Main street for rope drop. Rope drop was promptly at 7 a.m. People RAN (despite CMs calling out, "please don't run!") directly to Nemo. We made it on the first sub. It was INSANE. Too much fuss for what is essentially a cute ride. I would not waste an MM on it again.
Now, this was during spring break, and there were record crowds. It will likely be not so busy when you go.
There has been some speculation that the initial crowds may actually die down just before the end of MM. Hydroguy was trying to get some feedback from recent riders, as to whether it's a good strategy to get in line for Nemo at, say, 7:50 a.m. on a 7 a.m. MM., just before the regular crowds hit. I haven't heard any consensus on that, yet. If that is true, we're talking a 45 minute wait instead of an hour or 75 minute wait if you get in line at say, 7:15.
Some people say that if you can stay late, the best time to ride is just before the park closes-- because if you are in line 5 minutes before closing, you will be able to get on the ride; they'll keep it open until everybody in line has gotten on. So that's another strategy.
By October, maybe the fuss will have died down some anyway, and the wait won't be as terrible as it's been since it opened last summer.
Anyway, long story short, I wouldn't use my MM on Nemo. You can do all the rest of the rides during MM, including Space and Buzz, if you skip the subs.
Hope that helps! As always, read Hydroguy's sticky thread for the best info!