I think the very first step is to identify which items are considered "structual change", which are "design centre upgrades", things like "raising the fireplace", enlarge basement windows, hardwood stairwells, 3-pc rough-ins, change entrance door from single to double, etc. are all structual changes, it's better done with the builder as they are much more difficult to do afterwards. The design centre upgrades are easier done after you take possession, such as painting, hardwood flooring, add in more potlights, etc.
Speaking from our own experience, I'd recommend the following,
1. upgrade basement window as large as you can.
2. rough-in for the basement
3. central air with builder
4. don't go cheap on the kitchen, definitely get crown moulding on the cabinets
5. spend on ensuite bath. Both kitchen and ensuite will give you the biggest bang for your bucks.
6. smooth ceiling? I love that too, but too expensive.
7. gas stove, get builder to hook up the gas line into kitchen.
8. centre vanity light box above the sinks, if you want to replace the vanity lights later on.
9. if your garage door are two single ones, change to one double door, you will have more wiggle room in and out of the garage.