This is for a 2.1 channel setup.
I find the integration between lows to midrange are hard to blend.
Compared to 3 way alone, the sound is more natural with a 3 way.
It's a little easier these days to integrate a sub with the phase alignment on some subs.
I have the Paradigm Seismic 110 with room correction and I still can't blend it with the mains properly. I have tried other subs and the same result.
I've tried to use various subs with several speakers namely my old B&W LM1's and Martin Logan Vista.
I've also tried it with my 3 way speakers.
The three ways on there own sound better IMHO.
Now true 2 channel.
Have you moved any of the speakers, to make sure they're in the best position? Have you moved your listening position for the same reason? Have you walked around the room, to listen for spots where the bass is strongest and weakest? If not, do that before making your conclusion.
Placement and acoustics can cause the problems you have had integrating your sub with two-way speakers or any combination, really.
2.1 vs 5.1, etc is about speaker locations, not the number of drivers- it has nothing to do with drivers.