Definitely agree about head height and windows, you want to maximise the light. If you have dormers, put them over where you expect to get in/out of bed as you get a bit more height to stand up.
Also consider how many plug points and where they will be, make sure they are on the design.
The actual design of the loft conversion is often unchangeable early in the build, so make sure you are really happy with the plans early on.
Seriously consider how the roof would work in future if you wanted to install some kind of solar energy panels or tiling. Our dormers are on the sunny side, but we designed it in consultation with solar panel advice, and there is no problem to add the panels too when we have budget (which we do).
Heating wise, if you have a crap old boiler and plan to have central heating in the loft, think about capacity. You may need a new boiler and tank to sustain extra radiators.
Loft rooms are hot, hot, hot in the summer. And listening to rain on veluxes makes you think your are living in a tin hut. So consider if you want your main bedroom up there, some people I know built the room then cant bear to sleep in it. We built-in a small aircon unit as we want to be able to work up there all months of the year.
If you go with a dedicated attic conversion company it can be a lot more efficient but beware they may have a "template" solution and tell you things are impossible, that ARE possible, just harder work and not their usual design. Find someone willing to be creative.