1) How to work with clients and help them launch new ideas.
2) How to work quickly and efficiently to launch quickly, with no real responsibility for long term maintenance.
3) Lots of new technologies, based on what clients want and what helps you accomplish #2 quickly.
4) A healthy network of well rounded and skilled individuals in sales, design, and project management.
Now, here's what you won't learn at an agency:
1) How to scale fast growing systems efficiently.
2) Real systems engineering that makes things last.
3) Growth hacking techniques or anything else related to user acquisition.
4) How to hire and manage highly skilled individuals that can do all of the above.
In short, you'll learn different skills, some complimentary, some not. I think agency work is great for learning how to start a startup or a new venture, but it likely won't give you the skills you need to keep a company running and growing.
There's a lot of great work coming from agencies [1][2]. But there's also several agencies that are just doing busy work, making a living by getting basic digital production work done.
If you have an offer from a digital agency, I'd look carefully at:
1) the type of work you'll be doing (and, more specifically, which clients)
2) to whom you'll report to, and the experience of your peers
3) what this agency has done in the past, that you think would add value to your career.
Good luck! If you need help assessing your options, feel free to drop me a note. Email on my profile.
[1] http://en.wikipedia.org/wiki/Cinder_(programming_library)
[2] http://www.compositeframework.io/
EDIT: having said that, there's good things to learn on both. A startup teaches you to be flexible, and to move fast, be lean, focus on the product. Agencies teach you to scale things, to get the work done in teams, to work with enterprise clients.
- at a startup you learn how to make users happy.
- at an agency you will learn how to make clients happy.