I asked myself the same question. and the conclusion i came to was use what fits the project. Am just using ins and outs? do i want video out? have a network cable available? wireless ? etc, But more importantly where are you with skills. (i know you said you are past beginner, but i am adding my 2c for othefrs that ask the same)
I don't mind looking at data sheets and wiring things together so i rarely use shields and right or wrong i think they are more aimed at the entry / beginner market, and i am not sure that the entry level would benefit from the extra (functionality and headaches) the OS does bring.
My gen2 galileo was sitting on my desk watching whilst I completed 1 project using an Arduino and another using a Pi.
But If i was just starting out then i think its a good fit - Go the shield and sketch route to get you addicted and then when you get more confident then start digging deeper,
Alastair
P.S.
forgot to mention "can run windows". Now i must say that i have not tried this yet , and i must confess I am a Windows developer by the day, I live in and love Visual studio and am generally a Windows fanboy, but am really not confident that its going to be a whole lot easier. and please please please dont make my embedded device require gigs of updates. But i will be giving it a try.