A WAAS upgrade is 3k and change, it will shoot every approach you can shoot with the GTN boxes, some folks like the knobs too, airways are easy with a iPad for reference, just have to enter in one or two more things, I fly behind two GNS boxes at work and two in my own plane , in and out of some of the most busy airspace and and some gnarly weather too, always been quite happy with them.
Just upgrading one of your boxes will work fine, you'll just be non WAAS on one and loose the cross fill.
I would NOT sell both GNS boxes for one GTN, you're loosing a ton of redundence and loosing a second nav com, in trade for basically touchscreen 530 with a different GUI, sounds like a bad deal.
Good news is many folks know both the GNS and GTN boxes do the same thing, so you'll have no probalen selling them if you want to go down that road.
As far as transponders go, WAIT prices are going down and features are going up, being a early adopter never is a good idea unless you need to blow money for taxes or something.