Does this mean that having my walls open right now is not really that big of an advantage for home automation?
Not at all; having your walls open is a huge advantage. Wireless stuff is getting better, but I'd still rather have all of my security wired if I had the chance. And, with wired you don't have to be constantly replacing batteries everywhere. Plus, you have a chance to do some things that would be harder to do with wireless.
Make sure you get some alarm wire to every door and window location. You don't necessarily have to home-run every single window; daisy chaining the windows in a given room will be OK in most situations. If you have a window that you know you're going to leave open a lot, you might want to wire it individually. Do wire each door individually. And since you mentioned window treatments, make sure you get a separate run up to a top corner of each window opening where you might want to put in a motorized treatment.
Run at least one run of Cat4e to each room. If you have a place where you know you will have an entertainment center, run two or three. Also run one to each thermostat location. Run either coax or Cat5 to each exterior location where you might want to put a camera; also pull one or two extra coax runs to a south location on the house in case you decide to go for satellite TV or radio in the future.
Think about which doors you will routinely use for entry and exit; you'll need a keypad of some sort near each one so you can arm/disarm the security. Pull some alarm wire to the location in your garage where the garage door buttons will be, so you can connect those to your system and have it control the doors. Think about where to put exterior temperature or daylight sensors and run some Cat5 there. Are you going to have a lawn irrigation system? Pull some Cat5 to where its controls will be. Pull a Cat5 run to a location in each room where you might want to put in an audio system control pad.
One thing you may not need/want to hardwire is lighting control. There are some good hardwired lighting control systems available, but they tend to be expensive. And, in some areas, connecting the low-voltage wiring for lighting control to the line-voltage control devices is problematic from a code standpoint. Most people who use UPB have had good results with it (including me). UPB transmits signals over the power lines and doesn't require separate wiring.
Finally, a basic but often-overlooked point: Wherever you are going to put your controller, be sure to pull a dedicated branch circuit to that location. And a phone line.