We know from Voyager that the Borg transwarp coils were tiny. If the Federation had that kinda level of tech, the nacelles would probably only be there for the bussard collectors and maybe the odd, short warp-speed flight.
And while, yes, there were Xindi onboard Enterprise-J, they coulda only been there after the war started. Like how Cardassians and Jem Hadar started crewing each others ships.
And there's always the possibility that the Federation later allowed the Xindi to be wiped out because it meant they'd win the war against the Sphere Builders. Churchill (methinks) did it with the bombing of Norwich. He allowed the Nazi's to beat the **** outta the city so the Nazi's wouldn't know the British had cracked their encryption codes.
I also happened to like the Enterprise-J.
And they probably will switch to the NX-02 and give it shields and ****.