What would be your ruling if a Wizard wished to have an additional 9th level slot?
I'd rule depending on the general behaviour of the player.
Analysis: the players expand a temporary ressource (spell slot), an especially weak one since such an undertaking could be done during downtime, to get a permanent increase in power, potentially imbalancing the group. That's generally bad, but the check and balance is provided since there is the potential loss of the permanent ressource of casting Wish.
Case 1 (general case) : I'd go "by the rules". Even if the player isn't wording his wish like a lawyer-proof contract, the PC casting the spell most probably has top human intelligence and knowledge of how the spell works in the world, with a thesis-long theoretical background... So in general, I am not a fan of "twist the wording until the player hate you". I'd warn its a "non standard" effect, incurring the 33% chance of losing the Wish spell, but not try to impose this penalty ON TOP of being a dick. That would allow the player to get 4 or 5 9th level slot before losing the ability to cast Wish... At the very end of a campaign, does it matter this much? I'd correct any imbalance by giving a few more artefacts useful for the other members of the group and up the level of the opposition accordingly, but I wouldn't be a hostile. We're speaking "endgame" anyway.
I'd discuss the wording of the wish with the player however, to differentiate between the slot and the ability to cast a second 9th level spell each day, but not to screw the player. If it was somehow fitting, a side quest of recovering the notes of an old mage describing how to achieve this effect through Wish without risking more than the stress would be OK.
Case 2 (least likely) : the player has an history of using Wish in a creative way and is making an habit leaning toward becoming gamebreaking OR the player has found a way to circumvent the statistical limitation, either by Wishing "to be immune to wish stress without any detrimental effect to him including but not limited to loss of spellcasting ability, alteration to his personnality or physical form and reduction of fighting ability" or partnering with another spellcaster Wishing for their friend to regain the ability to cast the Wish spell after losing it due to stress (with the same proviso). The check and balance removed, allowing it would make the player spend the next 3 months doubling his 9th level spell slots through repeated casting of Wish... That's not a desired nor reasonable outcome. Then, I'd try to find a way to make the spell backfire, probably along the line of "You've exceeded the limit imposed by the God of Magic when teaching mortals their first spells, when limitation were imposed on the ability to alter the multiverse in exchange of being sheltered from its most eldritch beasts... Now that you have walked outside the sanctionned path, they noticed you..." (next adventure plots : how to get pardon? How to pass unnoticed from these creatures? How to ascend to godhood to be on an equal level with these creature? With so much magic in his head, he's bound to make some activate unwillingly as reality is constantly warped around him... At some point the PC could even Wish for losing his excessive ability)