The pros I see from LE 90 day certs are that commercial CAs will likely reduce prices on their DV certs. They may even go with free renewable 90 day or cheaper 1 yr. Both are wins for the internet as a whole.
On a side note, I am getting the impression that some on here think LetsEncrypt is trying to be a one-size-fits-all CA. I do not recall anyone saying anything remotely similar to that. There are a huge number of situations/configurations where LE will not and maybe should not be applied.
By limiting the certs to 90 days and the capability to automate, LE can fit into the largest number of servers where encryption, at its current price/cost would virtually guarantee no encryption would be implemented.
If it is too much hassle to deal with 90 certs on a particular configuration then I suspect the cost of a commercial cert (ie wildcard) is a minimal concern.