Congrats! What fun to be planning something like this together.........enjoy it, and understand that you'll both probably be a bit "feisty" some days thru the construction process. Just part of the deal; don't let it get to you too bad. 

Now, your questions. Story-and-a-half, split-level, and 2-story are all good in their own way. But "old" really isn't the issue. Local guy coming down the combine ladder after the last load of corn recently, hurrying down and facing out instead of facing the ladder (surely the only person who's ever done that*******)......caught a foot in the ladder and broke both bones in his lower leg. Absolutely no weight bearing for 6 weeks, crutches for at least 6 weeks after that, and 3 months of therapy. He's 43. There's no way that I'd build a house without a main-level bedroom and bath, and main level laundry.

My personal preference is to have the laundry near the bedrooms instead of near the entry/kitchen, but some disagree w/me on that. To me, packing dirty laundry from the bathrooms/bedrooms, thru the house, thru the kitchen to a laundry room, then reversing the process to put it all away just isn't fun. That said, our house isn't that way, and there's no way to make it so it is, but I wish we could. 

Spend the money now to do extra wide doorways and hallways and at least one larger bathroom on the main floor so if either of you are laid up, you can still get around. No fun to be laying in a hospital bed and someone else is at your new house remodeling it to be accessible for a wheelchair.  And speaking of hallways, try to manage the design to have as little square footage tied up in halls as possible. In my mind, hallways are wasted space that could usually be living space if the design was tweaked a bit.

We put a fireplace on an inside wall. DUMB! If you put in anything that requires a chimney, make sure it's on an outside wall.  

Pay close attention to your site. What will you see out your windows? Does it work to set the house at an angle on the site so you have nice views out each window?  If you think you might ever want an extra bedroom in the basement, plan for it now by either installing an egress window or siting the house so that you can have a walk-out. 

MHO...........do NOT do Pella windows. There are other brands that don't cost any more and are much more well-built and efficient. Research. 

Spend the money on the major things that can't be easily changed......foundation/basement, framing, windows, thin-coat plaster walls instead of drywall and mud, etc. Carpet, flooring, appliances, paint can all be easily updated later on as needed. Tough to fix a bad basement after the fact.

Tour lots of existing model homes, etc. and look at lots of floor plan books. Keep notes and take pictures of things you like and things you don't like. 

Have fun!!