witch ever way you decide I always loved the in-wall setup as you could have lots of room for tweaking and upgrading without the hassle of running into lack of space.
That said I could offer advice comparing my system to others I have seen.
things I like having
spacious aquarium back room
Big skimmer
(no preference as I have a DIY skimmer with bubble blaster 10000)
biggest sump I could fit in the space planned
I like the DIY even though sometimes its cheaper to get pre finished product
LED all the way (lots to chose from DIYs and I like radions,kessil and few out there)out of all I love my DIYs as I could tweak them as needed
outside over flow coast to coast box with double herbie.(for later modifications if needed)
water circulation I beleive the more the marrier
and like the hidden power heads or a couple larger water pumps into the sump(again for later modifications)
If going the route of LPS and SPS I will go with a at least triple doser.