I’ve been through this and to be honest I haven’t really felt the differnce between sets of wheels. I changed from some PX model B wheels which were minimal spokes, stiff and light to Ultegra hubs on Open Pro’s 36h and didn’t feel much if any difference. Maybe a bit of a smoother ride on the Open Pro/Ultegra wheels but I might have been imagining it to be honest.
Changing tyres can make a bigger difference. I’ve tried a few and I keep going back to Vittoria Rubino Pro’s which seems to be grippy, light, supple and puncture resistant all at the same time.
The biggest difference I have ever felt is changing framesets. I loved my Specialized Secteur but then I changed to a Tricross and it felt awful, dead feeling. Hard to describe really but I think I know what you mean! I swapped to a kinesis Racelight and that’s better but not as good as the Specialized Secteur.
Then, one day, I got a 1990’s Trek steel road bike for a friend and after I restored it for him I had a ride on it. Oh wow, it was so nice. More flexible yes, heavier yes, but such a joy to ride. I hated giving it to him!
So the upshot is…… I’m buying a Genesis steel road bike (TDF) soon. It doesn’t matter what things weigh or what spec the gears are IMHO. People are brainwashed into carbon carbon carbon, lighter wheels, faster faster faster! BUT let’s not kid ourselves, we aren’t fast even compared to a lowly Cat 3 road racer so saving a few grams here and there or buying fancier stuff doesn’t really make much difference to most people, even though they might tell themselves it does (with help from the media/shops/friends!).
Oh, and additionally, get a bike that’ll fit proper mudguards. Makes riding so much nicer round where we live!!