I have a (1995) 1700 sq ft Cape in north Maryland running a 1995 Rheem 3 ton (10 SEER?) and WeatherKing forced hot air oil burner (140k input!). I am the first owner, have not had one problem with this system - not one. To me, the cooling is decent - humidity feels ok when set around 76F. No issues on the hottest of days. This past month's electric (July) was $200 (but I have a turn back thermostat running from 6am-4pm). The oil burner has a .85 nozzle to increase cycle time. By far, heating costs far outweight cooling costs, but the heating season is longer. My small house has 8 of Andersen's largest residential skylights, and most (Andersen) windows run down to within a foot of the floor (lots of glass). That's probably not enough to warrant the likes of a 140k oil burner, but is an indication that this house has LOTS of glass.
So, if I am relatively happy with the existing system, even with the undersized return (and whatever else in the duct work is poorly designed which I do not know about), should I really be concerned with duct work mods at time of new install? Will the expense easily be paid back in 10 years or too hard to answer with this limited info? The plenum and main are made from that crappy duct board - that could be mod'ed easily. But the house is a Cape, and getting to any vertical runs would be prohibitive (most interior walls consist of 3/4" pine tonque and groove over drywall).

I've even used one of those Lasko drum humidifiers in the winter. Never any issue (that I know of) with the ductboard. No smells, I'm never sick. I thought for sure that humidifying that ductboard would create some nasty mold; if it is, I can not tell. So overall, I feel I've gotten away with many 'improper' system design issues, yet I am reasonably pleased with the performance.