The good news is that for the most part, you don't really need to decide on hardware yet. So you want an alarm - it will generally be wired the same whether you decide to use ELK or another brand. But you need to sit down with a drawing and figure out the placement for each window sensor, door sensor, motion detector, (perhaps occupancy detectors too), glass breaks, keypad locations, speaker locations (for the alarm specifically), door bell interface, etc, etc, etc.
For lighting, the biggest thing to make sure is that your electrician knows to run a common wire to all the switch locations. Then they will run the switch leg to the light. That is fairly common practice today, but it use to be common place to run the power (with common wire) to the light and only run the switch leg to the switch. This leaves you without a common leg at the switch. Most "wireless" lighting systems need the common wire at the switch.
Again, I would dream big and wire for things that you may never actually do. Things like intercom system, CCTV, digital phone system, water leak detection, HVAC control, weather station placement, pool/spa control (if you are planning on putting one in), outdoor lighting control, driveway detection, outdoor PIRs, automation system (like location of touch screens), etc, etc, are easy and pretty inexpensive to wire for during contruction, but might be cost prohibitive later on.
You'll never have a better opportunity than when the house is being built.
