• low pay, even by nonprofit standards
• very long hiring period
• internal innovation is not as easy as you might hope
• mixed reviews about reputation, depending on who you ask
More detailed explanation:
"Lack of funding" was the almost guaranteed answer to any suggestion for improvements or new ideas while I was there. I hope it was because of the especially-down financial period we were in at the time and that it has changed since. I felt like I'd be in trouble rather than appreciated for scrapping to go find money for it, which was frustrating and disappointing even though there were logical reasons. I hope they are open to supporting more innovation within the organization now, but that requires funding as well as encouragement, and funding always seems to be desperately low.
A 3-month hiring period would be unusually short. From application to acceptance (or rejection) is more likely to take 6 months or longer, and many people have had their long and hopeful interview process end unceremoniously abruptly, which made them feel pretty bitter toward the organization. Certainly apply, but temper hopes and any time-dependent plans.
Ashoka pays at the bottom end of even the non-profit scale, so you should be realistic about this. The work is fulfilling and you may get residual benefits beyond your time at Ashoka, but unless you are top management, you'll have to live frugally and may need a second job for extra comfort or savings. That's hard to do because long hours are often necessary. Married or coupled employees have an advantage in being able to earn less at Ashoka while their partner earns more elsewhere. It would feel better if Ashoka compensated people better, but the fact is they get great people at a discount because of their reputation and applicants' strong desire to work for them, so there's no need to pay higher. A hard truth that unfortunately makes logical sense.
While most people still react positively to the mention of "Ashoka," don't be surprised to hear mixed reactions, including comments about "founder's syndrome," money-starved actions or motivations, a sense of a "dinosaur" organization coasting on past reputation and even a bit of hypocrisy for not practicing internally all the same values they preach outwardly. As in any case, many of these things have reasons, nobody can have a perfect world and organizations are made of human beings, after all. Just don't put too big a halo over your view of the organization.
I would still recommend working for Ashoka--I really enjoyed it and value my time there, especially the quality of work and people. But I probably went in with too much idealism and optimism, so I felt more disappointment when I met the realities of the job. You'll face the same challenges here that you would face in any other job, especially cash-desperate nonprofits. But the quality of mission, work and people at Ashoka is higher than most.