No one was arguing he should be rated at what Miggy is. They just said that if Miggy can be a bat first player and be a 99, why can't Cruz be one and be at least a 93. Miggy is rated 99, likely above 99 based on what the devs have said in the past regarding how the overall rating is calculated.
If you look at the ratings increases/decreases this year there have been plenty of players who got significant upgrades when their track record is questionable. Look at Kipnis and how offensively is is basically rated the save vs RHP as Cano. Yet Kipnis put up less than replacement value in 2014 and Cano has been an MVP candidate throughout his career.
The ratings increases lately though have been pretty lackluster and conservative so I don't expect any movement on Cruz or many of the other players everyone and myself as well have been saying could go up. It's why I don't "invest" in cards since the profits aren't guaranteed like other methods of making stub profit.