I have to agree that Manuel Antonio is a must-see. We were just there, in peak season, and it wasn't overcrowded. It's busier than most of Costa Rica, but there's a good reason for that. To say it's "one of the most overcrowded areas I have ever been to" is a bit odd for someone coming from Los Angeles. Depending on what hotel you stay in, sightings of monkeys, deer, and iguanas can be virtually guaranteed without even leaving the property. The beaches in the park are spectacular, and even Playa Espadilla just outside the park is very nice.

With 2.5 weeks I'd get to Arenal, Monteverde, Manuel Antonio, and maybe one other destination of your choice. A night or two in Alajuela before your return home is a nice way to see "real" Costa Rican life in a mid-sized town with a great town square, and just a few minutes from the airport.

We rent a car when we go, but as Dman notes you have to be alert when driving in CR, and get the insurance. The roads are generally way better than they were even just a few years ago, but driving there is still somewhat unpredictable. And don't drive inter-city after dark.