Get them refaced and change out the hinges and pulls. If it were me, I'd paint them the same as the wall color.

Do you have the missing shelves? They will make it much less awkward.

I think the built-ins are a pretty good use of that space, though. You have a cabinet maker? Have them put in cabinets more to your liking. I don't think it would be worth refacing these if you don't like the open shelving area. Just do it right, the way you want.

Getting rid of them altogether is a cheap option. Don't let the HVAC hold you back--it's probably a very minor detail you can deal with when fixing the drywall. (see if the flooring goes under the cabinets first!)

What about trying to cut down the center unit and changing the countertop to a nice wood top? Maybe even making the upper pieces on each end into bookcases instead.

Good luck!

Connect the three upper cabinets with a top piece to make it all feel like one unit. Add wood shelves to the two open voids. Paint the whole unit including the walls behind added shelves one color such as Benjamin Moore's Revere Pewter.

I think if you paint built-ins the same color as walls, they would not so pop up.