If somebody starts talking about doing all your ductwork in flex,that's the 1st sign to show them the door.
That's a fact. The high pressure drop thru flex pretty much guarantees that an all flex duct job will be near impossible to balance.
Re the inadequate return size, if the sizes listed are duct sizes then you've got plenty of return. If they're just return grille sizes then you have to look at the actual duct sizes to see whether or not you actually need more return. FWIW, the average ram and slam all-flex contractor types couldn't actually calculate required duct sizes if their lives depended on it.
With properly designed ductwork, its fine to have the unit at one end of the house. My house is single story, 2200 sq ft heated plus a double garage at one end. The air handler is above the garage near a pull down stair. Sheetmetal ductwork sized for constant pressure drop, with 1/2" liner for noise and 2" wrap for insulation runs the length of the house. Takeoffs with balancing dampers and 10ft or less flex runs to ceiling diffusers. The system is 90% self balancing with only a couple dampers throttled a bit and the rest wide open. I have zero fan noise and zero air noise anywhere in the house.
Re the current ductwork... Have you stripped off any of the wrap to see if there's anything wrong with it, or is it just that the wrap is in bad shape? At 22 yrs, the wrap likely could stand to be replaced. Hard for me to imagine the ductwork itself isn't salvageable with a bit of work. Loose snaplock joints can be fixed with a few self drill screws. Tighten up the joints and tape all of them with good quality duct tape to stop leakage. Wrapping ductwork ain't fun, but you can save yourself some money there and probably do a better job than 90% of the "pros". In any case, you'll have a far better system than you'll get from some hack that doesn't know anything but how to string out 50 boxes of flex.
FWIW, I worked in the business for 15 yrs quoting and running commercial and institutional (schools, hospitals, etc) jobs from $20K up to roughly $900K. Based on that experience, I can safely say the job they're quoting at $22K includes about $14K in pure profit.
