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Depending on the timing of your trip and the kind of snow year - those higher passes are often snowed in much longer than Cottonwood as well. This year shouldn't be an issue though based on the lower snow year and how quickly much of the Sierra is melting out. but the snow on Army/New Army is often another piece to factor in along with overall mileage/gain plans. =)

Got it. But they are both eligible for continuing on to the JMT, right?

In a 3 week hike, I don't know that 1,000 feet of extra climbing makes much of a difference, but I have not really looked into that much detail yet. Thanks!

If you decide on the Cottonwood Lakes option, then you'll need to traverse either Old Army Pass (12,000ft) or New Army Pass (12,300ft), both of which are significantly higher in elevation compared to Cottonwood Pass (11,140ft). An advantage of Cottonwood Pass is that its trail connects with the Pacific Crest Trail (PCT) right at the top of the pass. I find Cottonwood Pass to be a more manageable option compared to the other two passes, especially when carrying a heavy backpack up and over the pass.

Hope that helps!