Scoot: we'd visit Arenal, Tortuguero, Corcovado, Manuel Antonio and Puerto Viejo, though not sure in which order yet.

ellen: i really don't get what you are saying here
".....The thing is we're not planning to make reservations for hotels too much in advance, and apparently they need to know where you are staying (of course). "
are you not planning on making any reservations at hotels or what? can you elaborate on this a little.
also - if you go to the interbus website and look around a little, you will become more familiar with the whole concept.
as for reservations for the shared van shuttle - some routes are very popular and fill up fast and others you can make a last minute reservation.

No, we're not planning on making all hotel reservations in advance. I asked this a while ago here and most people said it's not necessary due to low season. We'll have an idea about where to go of course, but we like the option of staying 1 or 2 days longer somewhere if we like it.

reservations on many shared van routes can be made a day or two in advance, if necessary.
also - in your original post, you mentioned taking domestic flights between arenal or tortuguero or puerto jimenez. check with sansa and nature air -- with many domestic flights, you will have to fly to san jose first and then transfer to another flight.
if arenal, tortuguero and puerto jimenez are your destinations, i would recommend taking the shared van shuttle to arenal, rent a car there. turn in your car in arenal. take a shuttle to the boat landing for tortuguero -- pura vida tours in arenal does this from arenal -- and return via boat/ shared van shuttle to san jose. take a flight from san jose to puerto jimenez and rent a car there..... or not.
of course, if you have a rental car, it does give you more flexibility as far as picking hotels in an area. if you want to rent a car, you can do that and drive to arenal, drive to the boat landing for tortuguero - there is covered parking there -- and then drive to puerto jimenez afterward. if you don't want to drive to puerto jimenez, turn you car in at the airport and fly.

Yes, most flight go through San Jose, but if we pay a bit of attention the schedules seem allright.
One company mentioned turning in the car in Cariari (or something like that), I think that's near the boat landing for Tortuguero if I'm correct?

cariari is about 45 minutes or so from the boat landing at pavona.
quite frankly, if you are going to plan on turning in your car in cariari, why not just turn it in at la fortuna and take a shuttle to the boat landing? of course, if you want to do some exploring between la fortuna and pavona or make a number of stops, rental car is the way to go.
for your flights - keep in mind that nature air flies out of pavas - a suburb of san jose - and sansa flies out of sjo in alajuela.

the only place that i think you would really need one would be arenal. things are kind of spread out there and having a car is useful. by the time you pay for tours that include transportation and taxis, you could rent a car. keep in mind that the town of la fortuna is 20 km from the volcano and there are many very nice hotels that are close to the volcano and far from town.
otherwise -- it is really up to you. i hope you have more information now and you can make a more educated choice.

I think we'd best get our itinerary right first (i.e. the order).
I'm thinking we'd better keep Arenal and Tortuguero for last as they seem a bit more relaxed/laid back than Manuel Antonio/Corcovado (where more demanding hikes can be done), or am I mistaken here?
For the mini vans: any idea which routes are the most popular (i.e. need to be reserved in advance)?
I see no reason to fly to anywhere in Costa Rica other than Pt Jimenez for Corcovado, though with 3 weeks you can work your way down the coast via Chirrpo (closed in May) and Dominical/Bellena. But you dont need a car there unless your headed to Carate for a base IMO, and you need a SUV IMO with 7 rivers to cross to Carate.
Tortuguero is best accessed without a car, go via bus or shuttle or a tour.
The central areas like Arenal, Monteverde, Rincon, Celeste, Cano Negro are best explored on planned route, 1-2 nights at each.
You can rent cars oneway, but if its a far locale to drop, you will pay a large drop fee.
If you want to explore 3 different areas of the country, break up the trip in sections, and put the beach last IMO.
Get car and explore Arenal/Celeste/Rincon areas, drop car in SJ and fly to Corocvado 3-5 nights, then fly back, and then head to Tortuguero and Caribe, no car needed.
You can raft your way from SJ area to Tortuguero via the Rio Paquare and get dropped for boats to Tortuguero.