I think it depends a whole lot more than simply 3 speakers v 2 speakers (per side).
Have you changed makes/level of speaker, for example if you started with say the DLS R6s and upgraded to the UR6-3i then that upgrade could be the cause of the differences, not the fact that you now have 2 more speakers.
It is much harder to get a 3 way system installed as well as a 2 way one. The differences you had can be affected as much by install as by the speakers involved, whilst you have them well set-up for focus, you are missing some aspects which make them more musical.
I'm sure someone will coma long and give you some guidance on what needs to be looked at but let's start with a kit list. What have you got installed now and what did you have?