I can see some possible issues, too. If you want to take a hard line approach, this breaches net neutrality just as much as slowing or charging access to other sites. Sure, Wikipedia is already the defacto source of information for a lot of people, but this would cement a monopoly as such in those areas. This all sounds a bit silly when talking about Wikipedia, but it has implications for other services.

What if google or bing made a similar deal? Or any large corporation, for that matter? You set up an internet where the majors can buy their way into a monopoly position, not by convincing ISPs to degrade other services, but by convincing them to charge users less to use your service. This makes it harder to impossible for new companies to enter those markets.

All that being said, I think this (Wikipedia Zero) will be a net-positive thing, and I hope they succeed. I do see that this type of thing could have worrying implications for net neutrality, but ultimately they're not the first site to broker "free access" deals with mobile carriers.