Voyager was state-of-the-art at launch, so Starfleet is unlikely to have recalled her sister ships for a refit just to account for 5 years of minor tech improvements - the only more advanced ships at the time are the Sovereign and the Prometheus.
We don't really know how old either of those two types is in comparison with the
Intrepid. For all we care, half the Starfleet is "advanced" and "cutting edge", and those ST:FC ships are brand new designs all. Or then the registry numbers are telling, and the ST:FC ships all nicely predate TNG and date back to the old Cardassian War; the
Prometheus has been undergoing tests since that old war as well; and nobody can tell how old
USS Sovereign is since her only known sister ship has a nonstandard registry.
And what did they really have on the Intrepid? Quantum torpedoes (would show no visible change to the Bellerophon even if she did have them), ablative armor (in the case of Prometheus) - likewise and regenerative shields (again, only on Prometheus and again no visual change to the ship even if so equipped).
Funnily enough, we have never seen a quantum torpedo launched from a standard tube. The
Defiant and the E-E both have tubes dedicated to this weapon type, never seen firing anything else, and then separate tubes for firing regular photon torpedoes or other nondescript stuff. There were no special tubes in evidence when the
Lakota packed quantums in DS9 - but she never fired any, so we can't really tell.
Whether regenerative shields are a new thing is unclear, too: the computer just rattles out a series of technical specs, without claiming that these would be special to the
Prometheus in any way. It may be like a brochure saying "our tank has composite armor and subcaliber antitank ammunition" when every tank on sale has that. After all, we have never seen a starship shield that wouldn't regenerate!
Ablative armor (in tactically decisive amounts) seems nonstandard, though, as there's dialogue to that effect in "Paradise Lost". But if Starfleet gave none to the
Lakota in that refit, and didn't expect the
Defiant to have received any, either, then
1) neither the
Voyager nor the
Bellerephon would necessarily be recipients no matter what, and
2) if they were, it would apparently be a matter of requisitioning the right spray cans and doing the required two hours of spacewalk, after which nobody would be the wiser as to whether the ship has the armor or not.
On a separate note, why would the ship going to Romulus need to be particularly advanced in any front? Starfleet wouldn't want to give up any techno-secrets, now would it? We get the general impression the
Intrepid might be fast (Stadi sort of brags on that and Paris appears suitably impressed), which is good for a courier ship. But that's about it for requirements.
Timo Saloniemi