Think of it as it is your money; your building and you're living or working in the place for years, then try to get the best out of your money.
Don't forget, think of it as YOU are the maintenance guy, and YOU're the accountant paying the bills.
There is also a new term in the industry - "RIGHT-SIZING" that's worth keeping in mind.
Prepare a control system and sequence of operation early in the design - Because if you can CONTROL IT, YOU CAN DESIGN IT. Sometimes, you can down-size substantially with controls (DCV, CO2 sesnosors, occupancy sensors, diversity factors in load calcs when applicable, etc)
Be a team player, i.e. educate the architect early on to get the proper space (without exageration, remember, it's your money), explain and volunteer different ways to the architect. Most anymosity between Architects and Engineers comes from lack of understanding of each other's trade.
as pipesnpumps said above - be responsible, don't rely on others (vendors) to design or chose a system for you.
You got the last one correct - Ask questions, Talk to your Peers - as you just did.