Pretend you are walking around the rooms in your head. I've helped a few people with plans but could never do it for myself cos I'd drive myself doolally with my perfectionist ways.
Watch wall space; keep an eye where radiators, doors, windows are going. Will there be anywhere to put furniture that is not in the way of something?
Having lived in houses with and without concrete/hollowcore floors, I cannot stress the wonderfullness of them enough. I've been told it's a pain re wiring and plumbing but nothing ever happened me and that stuff is always a pain as far as I can see. For day-to-day living it's the bees knees. It's quieter (v. v. important!), warmer and makes the whole place feel really solid. People who haven't lived with it don't really appreciate just how big of a difference it makes (IMHO).
Watch dormers; they are space inefficient and the light from the cutesy windows is usually rubbish. Too much roof-hipping can make headroom a bit of a disaster and make furniture hard to place; often making small rooms smaller. Velux are much brighter but rain on them can wake the dead. Make sure your architect is firing on all cylinders for that part.
Don't leave the small windows on the North-facing wall or the rooms will seem even more dull/cold. Light is one of the things that really make a house for me, so it would be something I would spend a lot of time on; lighting at night, aspect of house, window placement, size and design etc.
I wouldn't let the architect go mad with all sorts of weird room sizes. Carpets, furniture etc come in fairly standards sizes and unless you are loaded custom making is expensive (or wasteful or both). Keep an eye on rooms with extra corners or corners cut off; they can look great but can be a bit pointless as regards effective space usage. Halls and landings are great if spacious and give a lovely airy feel but there's no point in having a huge landing and a small bathroom or a huge hall and a cramped TV room.
Downstairs loo; lots of new houses have it off the utility to save kids traipsing through the house if they are playing outside (or so I'm told). To me, this is daft and it would make far more sense to have it off the hall so guests could go to the loo without you having to either tidy the utility room or send them upstairs where they might a) wake half the house or b) get nosey in themselves. Make sure you have a cloakroom/cupboard.
I'd be thinking about open plan v seperate rooms type of issues too at this stage. Things like do you want the kitchen and dining area combined or the dining and living area. Lots of people go for the former, I far prefer the latter.
I'd also be thinking about what you spend most time doing; watching TV, reading, cooking, bathing/make-up or whatever and make sure that you dedicate lots of time to thinking out that area.
If it's 4 bed, will there be a room downstairs for a play room or study? If not, will the downstairs be adaptable re extensions down the line (I know, I know, you're only building it) because in a dormer expansion is going to be a little more difficult.
You've probably thought of most of this yourself but I'm having a very quiet day at work!
Rebecca