Without further additions to Masamune at 95 (beyond just base damage and 5 more strength), Amano will easily beat it.
In near acc capped situations, Masamune 90 still beats Amano, however that edge is lost whenever Amano's acc starts to actually help (as mentioned in Voidwatch). I saw draylo mention he didn't have accuracy problems in VW, which makes me think he's either never done VW, full of ***, or really bad at parsing.
As for other relics:
Aegis annihilates Ochain on just about everything you'd bring Pld for, and though I can't see them going all the way to 50% MDT on Aegis (Since you could then be magic immune), Aegis already makes Pld nearly invincible on harder fights. Ochain still has it's place (newer Mnk type mobs, large groups of mobs, etc), and a good Pld should have both.
Kikoku: Blade Metsu needs a good more boost to catch up with Blade Hi. However, much more potent WS upgrades and/or another WS added in at 95/99 would hurt Kannagi a lot.
Bravura: I've yet to be really impressed with this, when comparing it to Ukon. RR is just crap in all situations compared to Fury, and MT is still lacking as well. I think Ukon will still hold out as the best "DD" weapon for War, even beyond 95, but we'll see.
Spharai: VS looses a lot when you're not at 70-90% crit hit rate, but is still superior to final heaven (at 90). With another WS damage boost and increased counter rate/attack, Spharai should bridge the gap pretty easily.
Excal: Still annhihates Almace in DPS on anything you'd bring Pld for (something that doesn't have paper defense).
Other's will depend on WS damage boosts and what happens to WSs/JAs at 95/99.
The big thing that has me worried for Empyreans in we are nearly guarenteed to get another WS otw to 99. If those WSs are better than Empyrean WSs, then most of the Empyrean weapons will lose a LOT of flavor. Especially if relics can use those new WSs.