Nerfs I see happening with high likelihood:
atma drop rate increased to above 50%
atma book cost decreased to less than 200 "current" tomestones (whatever they may be)
faster repop of atma book FATEs
reduced number of enemies required to kill for atma book
reduced cost of alexandrite maps from tomestones and allied seals
reduced amount of light needed to progress to nexus
Zodiac weapon dungeon item drop rate increased to above 30%
Zodiac weapon tomestone requirement reduced by at least 1/2
Zodiac weapon GC seal requirement reduced by at least 1/2
Zodiac weapon gil purchased item requirement reduced marginally

Nerfs that are possible but not as likely:
reduced number of dungeons to run for atma book
extremely easy way to "farm" alexandrite in large quantities, such as much higher drop rate from FATEs, purchased directly with gil/GC seals/tomestones, or guaranteed/high % drops from dungeons
reduction of nexus light requirement to 500 light or less
reduced number of dungeon drops for Zodiac weapon required

Nerfs which are extremely unlikely:
reduced number of atma required
reduced number of atma books required
reduced number of alexandrite required
reduced number of HQ crafted mats for Zodiac required

I think a possible solution to the Zodiac weapon continuation in 3.0 is an "alternative" quest that is available upon the release of the main Zodiac quest in 3.0. The reward of this quest is a fully upgraded Zodiac weapon with the same name as the final Zodiac weapon from 2.x but with the original stat distribution of the vanilla relic. The "punishment" for players who took this shortcut is the fact that their fully upgraded Zodiac weapon will have terrible stats compared to people who customized their weapons properly by doing all the 2.x quests and will not have the opportunity to recustomize it until much later in the 3.0 Zodiac quest line.