The first item you need to consider is the life span of the new hot air furnace heat exchangers, [censored] short cause they are about as thick as aluminum foil. Yup, they're efficient as all hell, but expensive to replace. A boiler, on the other hand will last about 25 years. The baseboard system will outlast 2 boilers.
Second major consideration, the ducting system for AC should be totally different from the heating duct system. They need to serve different functions.
I have hot water heating, baseboard, with a seperate ducting system in the attic for AC. It's far more energy efficient than a coil in the furnace. There are also systems available today with individual evaporators for each room. If I was doing the job today, I'd go that way, probably with a ground loop condensor system.
Another consideration is getting rid of accumulated heat in the attic. Most contractors want to sell a cheap fan that is thermostaticly controlled. A better way to go is a fan that is clock or sunlight controlled. Remember, insulation only retards the flo of heat, so cooling the attic thru the night gives you alot better energy situation in the first half of the day, the sun needs to totally reheat the insulation, before the ceiling can reradiate the heat into the living area.
The initial cost of the system is only one consideration and usually turns out to be the least part of the cost of heating and cooling a house. It doesn't take a lot of brainpower to install the systems today either, most of the "professional installers" are 19 year old kids with the brainpower of a gerbil.