Let's look at the issues.

1) Security: With the revelations about the NSA and corporations, plus the fact that many of the encryption standards may be compromised and much of the hardware/software is probably backdoored, do you trust anyone else with your data?

2) Uptime: If the SaaS goes down you are down and have no control of when it's up.

3) Billing and license costs. The cloud may be good if you do need to spin up large machines for specific season or jobs, but you still are paying for it. If you can't afford the expense of admins, you are at the services mercy to admin for you. If you are locked in to a specific service/configuration what happens when the Redmond license fairies give the gift of higher prices?

4) Goodwill of who's in control of your cloud. If the cloud provider decides to migrate or deprecate the software you need, what's your recourse? If you need to run additional software and they don't allow it, what's your recourse? If they are bought or decide to quit hosting the service, what's your recourse? Do they manage backups properly? Do you have enough bandwidth to back it up or load large data? Can you easily migrate?