I did a complete gut job when I bought my house 5 years ago (small cape) and I'm in the process of a large addition/extension job (adding 3x living space +full attic and basement) so I've seen a lot. I have a lot to offer. Not sure if I have time to go thru everything but I'll throw a few things out there and feel free to ask re other areas.
-First I have to agree with ckmk47- definitely try to plan for the future. Some areas that I did this is 1)when I put in a new boiler 4 years ago, I got one with a BTU that is capable of handling my future square area (I don't have to put in a new larger boiler now so I'm saving about $8k now) 2)5 years ago when I put in 2 bathrooms upstairs, I put them in a place that will now be in the right location for my extension (I don't have to put in new bathrooms now so I'm saving over $30k) 3)With my project now, I'm adding a 2nd floor and an attic. I'm making it a Masford roof (google it) so in 5 years if I want to add rooms, I have a complete floor to work with (another 1300sq feet). On a similar note, I'm also running electric and dead plumbing (including HVAC) up there so if/when I do finish the attic, I dont have to break any walls on the lower floors to do that work. On a similar note (again), I'm making a 7'x6' walk-in closet (aside from the regular closet) off of the guest bedroom which is back to back with one of my bathrooms. This WIC will also have dead plumbing so it will be easy to convert to a future bathroom, if I want.
-In regards to heating I researched and came up with the following-up until now my house had radiators and baseboard. Now that I'm putting in a 2 zone HVAC system, I'm switching the heating to a hydrostatic system (google it) (costing me an extra $2.5k). The advantage of this is 1)the forced hot air is not dry and 2)it is supposed to be more comfortable and more efficient. Radiators/baseboard is good except that a few of the rooms are relatively small and I don't want to take up wall space. And I agree with sguitarist18 re radiant heat.
-When I did my work initially, my contractor convinced me that it is worth adding a master bathroom, even though it took up vital space from my bedroom (to the point that I wan't able to put more than 2 twin beds and a dresser in there). I think that was a very smart move and I don't regret it at all.
-If possible, use 12/2 wiring, even for lighting.
-If you're making an extension with a basement, give the basement at least an 8' ceiling with regular windows (even if you're not finishing now).
-DON'T get chinese kitchen cabinets. When I did my work 5 years ago, the Chinese sub-contractor told me that they are top of the line in China. Half a year later, three cabinet doors are warped (although no other doors warped since then so maybe it was just a bad batch).
-Personally, I'm hooking up a few things to wifi that will then be able to be controlled by my smartphone). This includes 2 thermostats (thank you DanDeals) and public area lighting (like the LR, DR, and hallways). Then I could set the shobbos schedules very easily (when I did my work 5 years ago, I installed a fancy timer switch for my living room but I never figured out how to use it but this is much easier supposedly).
-Run RG59 (cat5e network cable) all over the house. Way more than you currently need. Almost anything could be run off of it. I'm running my cameras, intercom, phones, alarm, and wifi through those cables. To give you an idea, I'm running a minimum of 5 cables to each room (intercom, camera, computer, phone and extra). No, each room will not have an intercom and camera but I want the capability to easily hook one up in any room in the future (for example if I put a baby in a room, I'll be able to easily plug in the intercom and/or camera to use as a monitor).
-If you are capable (somewhat handy), run the network cables yourself. You'll save a lot of money. Youtube is your friend here and it's really not hard.
-Simliarly, you could save a good 2 or 3 thousand dollars if you set up your CCTV yourself (as well as the alarm system). If you by the kits, they are really user friendly.
-You could save tens of thousands of dollars if you're able to do most of the electricity yourself. My contractor is including all outlets and a handful of fixtures but many don't include either. At a price of $125/piece (normal price charged by an electrician , it could add up very quickly. Depending on your local, you may need a licensed electrician to sign off on it.
That's all for now. I have a lot more but it's erev YT and things are starting to get busy.