Let's add some challenges
Strategy alignment
To properly design an enterprise architecture requires a decent feel of where the company is headed, because, surprising as it may seen to some, that determines in large parts what demands will be placed on the infrastructure and (also rather important) what budget there is to make that happen. An IT strategy must match the business strategy - and will also require adjusting (and a budget for that) when the business focus changes. Nothing is ever set in stone, so plan for flexibility.
A simple example of change is a business decision to start an acquisition cycle. Good IT design can shave whole months off the integration process of a new business.
Note: don't expect an IT strategy in a startup, until they reach stability or find someone throwing money at them it's pretty much a case of duct tape and borrowed kit, and forget about boring stuff such as the mentioned license management, change control, backups that actually work and are tested, security or privacy. Going from startup to "proper" managed IT is always an interesting challenge. Some never get there (no, I didn't say TalkTalk or RBS out loud, did I? :) ).
Business continuity integration
Many businesses see BCM as an IT issue, which it very much isn't, but that is not to say that IT doesn't have a role to play too. A typical set of business crisis scenarios MUST integrate IT, also because plans have to be made for the absence thereof and ways to either fix that ASAP or cost out the consequences and see if that is an acceptable risk or needs insurance.
Note: if you work for a company that fobs off BCM to the IT department, do your own disaster planning and make sure you can find a new job fast because when things go wrong they WILL kill the business stone dead.