VP gear should award normal mode gear (heroic mode in WoD). If they added some for SoO, it should be 553. VP gear being higher level than flex/LFR is not a bad thing, especially in the case of LFR. If you've raided the previous tier, you should never even get possible upgrades from a new tier's LFR. I doubt Blizzard would ever do that though, because LFR usage would plummet like a brick as soon as it ceases to drop semi-useful gear.
VP gear being better than flex level is questionable, but VP gear is generally less optimized and has a limited amount of gear slots. Only ToT had large amounts of Valor gear, but most of it was terrible with excessive amounts of hit/expertise.
The best implementation of Valor/Justice was during Dragon Soul. The best pieces per slot (weapons/trinkets/tier) came from raiding only, with the only downside being boss-shared loot being exceptionally rare (I only ever saw one Vial of Shadows drop). Valor offered a limited amount of gear of normal mode quality, with one piece being BoE.
For a raiding character you might buy a few pieces before you'd be in all normal mode gear from raiding. After that you could buy Valor gear for off-specs, or buy the BoE piece for use on alts or for selling it on the AH.
For alts the system was a god-send. You'd queue up for dungeons where you'd get Firelands-level gear, including weapons and trinkets. Along the way you'd acquire JP and VP, which you used to fill out remaining slots (JP) and for upgrades (VP).