1. Visit Mt. Airy Bicycles in Frederick. Alternatively visit College Park Bicycles, their sister store but which has less stock. Mt. Airy sells Dahons, Bike Friday Tikits, Downtubes, and Bromptons. Every bike you'll want to consider.
2. The DC Metro allows bikes at off-peak times, and allows folding bikes at peak times but ONLY if they're in a "bag" and so are luggage. I've not yet tested whether my Tikit's cover (they look like
this) qualifies as a bag. Most likely it's fine. Anyway, this means if you're going on the Metro at peak, you'll (1) need a bag and (2) need a bike you can pick up and carry in that bag. And you'll need to be able to take that bag with you. So you'll definitely want test your bike in the bag before buying. I have no information about the MARC.
3. The classic train bike is Brompton. Folds very small, but uncheap. Consider them.
4. Consider a Tikit as well. If you're getting on and off THREE trains, then being able to fold fast will make a difference. The Tikit's transit cover is also built into the bike. It's not the smallest of the collection though. It will ride better than the others.
5. Downtube Mini is a possibility, though I'd personally look at the Dahon Curve instead simply because it has magnets.
6. 3 miles on a 16" is just fine. You'll be pleasantly surprised. You may find the Curve, Brompton, and Mini a bit squirrelly though. That's easily gotten used to. The Tikit will be better in that respect, but again, it doesn't fold as tight.