So I thought I'd revive this thread with a little bit of an update, and a "thank you" for some of the suggestions here. We're working with a great Integrator that made similar suggestions, and fortunately the build team has been taking their direction. The integrator was involved early enough (i.e. before the prints were finalized) that they were able to make some architectural in infrastructure recommendations (wall shapes, sufficient steel structure to hang a travelling PA, power tie-ins, etc) that are being incorporated. They've already done some modelling, and line arrays are out. They get that we're more concerned with coverage and good sound than looking cool
They're also being very proactive about building in extra cable runs, conduit, etc for our own future growth.
One of the things that has always been in the plans are multiple path-ways to the stage that are all on the same level (we've had enough of our own headaches getting things in and out of our existing building that we've always had that in the plans).
One of the things that I think made a huge impact for us was that a couple of our pastors were able to travel to see several of the systems that the integrator had done. They got to experience the full spectrum of installs from full blown to fairly modest, and I think they were educated well on what stuff is important to get right to start with, and what stuff to leave as upgrades down the road because budget won't allow us to do everything right now.