There is no room in my Soarer for routing the pipework for A2A. W2A front mount heat exchanger is easier to mount for my case. Smaller rubber water hoses are easier in my case than big hard air hoses to work with. (My car has hydraulic suspension - no room up the front.)
One of the things I like about positive displacement blowers is the instant throttle response - the super short air path of a W2A is desirable for me - I don't want to move all the air to the front of the car, cool it down, and then back again in an A2A system.
Factory cars use A2A for turbo cars and W2A for majority of positive displacement blowers.
It's not so much a case of which is "best", but what can work in each case. Factory installations are always a good guide of what can work AND reliable.
For me I like the Jaguar V8 with Eaton M112 blower and W2A system.:
http://planetsoarer.com/supercharged_jag/EatonMP112Jaguar.htm
I took some more pics of the Jag across the road:
http://planetsoarer.com/part3/index.htm
I guess the attraction of the Jag system for me (compared to a turbo system) - is I don't have to deal with excess under hood turbo heat, I still get that great V8 sound (no turbo muffling effect), nice simple exhaust, max torque from idle and no complicated pipework.
I also like keeping the stock intake air box and panel filter BFI etc.
What I don't like is the complicated intake manifold to be fabricated etc. Turbo installation is nice and simple up top - complicated down below. Supercharger is nice and simple down below- but complicated up top!!!!
With all my extra hydraulic plumbing a turbo was never going to work. I love turbo cars - I love the rush they give. I used to own an M90 supercharged Buick V6 in a big luxury car (no intercooling) - the instant low down torque is very desirable for me.
A2A or W2A - I guess each has advantages in different situations. For a boat installation of course W2A is the go.
Deciding between A2A or W2A depends more on vehicle type (hotrod, Soarer, custom install, boat, engine bay room etc) and Forced Induction type (brand/type of blower, type of turbo, manufacturer options etc).
I think a generic definitive statement saying one or the other is "best" would be a bit of a tough ask.