Yes, that's exactly the catch. Why should you require them to install anoter app if they might already use some other IM network? Approach of WhatsApp may be simplifies the initial registration step, but it adds to the global mess of the non interoperable IM networks. Negative impact way outweighs any potential comfort benefits, and authors who promote such things are to be blamed for it.
> Everybody with a phone already has one, so they don't have to do the whole 'create/verify an ID/password' dance
Actually you might want to do it, since numbers change, while IDs don't. Plus you want to authenticate the other party if for example you need a secure conversation (such as with OTR).