Unfortunately,
pre-defined major, lingering consequences for unorthodox uses of
wish by a simulacrum are quite limited, forcing you into the realm of "creative" solutions (which may come across as punitive/"unfair" if the player couldn't have predicted them in advance) or house-rule territory.
If you want to stick exclusively to RAW, then you'll have to get at least a
little harsh with the off-label
wishes. The simple options would be stuff like if the player wishes the BBEG were dead, then the simulacrum (and
only the simulacrum) gets teleported forward in time to a period where the BBEG is already dead, effectively wasting both the
wish and the
simulacrum at the same time. As stated, though, this risks coming across as punitive, as it's kind of the "nuclear option," but that is always a RAW fallback if you feel cornered. In order to get more specific, I would need to know more about the wizard as a character, the player's personality and style, and the overall tone of the campaign. If this is a comedy-relief character with a committed player (that is, a serious roleplayer who is actually playing a good, funny character) and the overall tone of the game is lighthearted, then silly or ridiculous results are very likely appropriate so long as they keep at least a little bit of the spirit of the
wish even if it's not quite what the player wanted. If it's a dour no-nonsense character played by a powergamer in a grim-and-gritty game, then you're probably within your rights to push the envelope at least as much as the player does, if not moreso.
Alternatively, this sort of trick could be known...and generally avoided due to drawing the attention of powerful entities. Be they humanoid spellcasters, immortal guardians of magic, lords of the fey, deities, underworld/fiendish beings, or entities from beyond the walls of reality,
someone will pick up on this sort of shenaniganery, and arrive to stop, manipulate, control, or recruit the wizard. This has the benefit that you can (mostly) allow the wishes to work "as intended," avoiding the biggest reasons the player might feel you're being punitive, but it comes at the cost of possibly feeling like a rugpull (if they're 17th level, how come they never heard of the Society for Preventing Alarming Magic Misuse before? Where were all these SPAMMers hiding?!), or of forcing the whole party to get embroiled in magic-political annoyances that they didn't ask for. Again, "harsh" can be in the eye of the beholder, but some may find "you nixed my perfectly reasonable rules interaction by making me jump through an endless set of hoops until I stopped" a reason to get upset. Your mileage will
definitely vary.
But let's say you're willing to depart from RAW. In general, when I depart from RAW, I either prefer to make it explicit well in advance, or I prefer to "yes and..." it rather than just saying "no," or if I cannot justify "yes" at all, "no, but..." and trying to be as generous as possible. In this case, the player has clearly found an interaction in the rules that works, so outright taking it away--or, IMO worse,
pretending to permit it while
effectively banning it via horrible over-the-top negative consequences--seems unwarranted. On the flipside,
wish is an extremely powerful spell (consider, for example, that Penny Arcade comic about the issues with the Deck of Many Things'
wish card), one that can easily harm the whole game experience if the player is allowed to ride roughshod over all semblance of logic, causality, or good sense. Some possible non-RAW tweaks to address the issue, of increasing severity (and, thus, stuff lower on the list should be reserved for more abusive usage/
wishes or players who refuse to 'play ball'):
- Any wish that affects the simulacrum (for example, by transporting it through time or to other locations) temporarily prevents the wizard from casting simulacrum again. When the simulacrum is destroyed, they will be free to use the spell again, but so long as it remains AWOL, the wizard is no longer able to use this trick. This respects the player's discovery of this interaction (the wish spells can still fire), but egregious wishes take away the ability to exploit this trick.
- While the simulacrum may take the risk of never being able to cast wish again, some amount of feedback still affects the wizard himself. Perhaps an off-label wish that strays too far could prevent him from casting wish for a week, or until the moon completes a full cycle, or until the next equinox, solstice, or cross-quarter day. (These are dispersed about 1/8th of the year around, so about every six weeks.) Or perhaps there's magical biofeedback from the wish effect, so any "spillover" damage the simulacrum experiences would carry over to the Wizard. Again, this respects discovering and using the interaction, but puts some kind of limiter on it. Obviously, the longer the wait, the harder this hits; a much harsher variant would step up the delay each time it happens, e.g. one week, then a lunar month, then the next solstice/equinox, then a whole year, a decade, and finally permanent.
- Simulacrum cannot sustain more than one simulacrum at a time; if you cast it while you already have any around, any existing simulacra are destroyed. As a result, one could argue that the wizard doesn't create different simulacra, he just creates the one simulacrum repeatedly, and thus the risk of your simulacrum being unable to cast wish again remains even if you yourself can still cast it. Potentially you could temper this by saying that gaining a level reverses such loss because simulacra cannot change, yet by definition a simulacrum produced by a 17th level wizard is different from the one produced by that same wizard at 18th level. (I'd argue that the harshest version of the previous option is harsher than this overall option, just for clarity.)
- There's a random probability that the negative consequences of a wish spell apply to the wizard himself, not his simulacrum, because the two are so similar. The softest version would be something like "roll a d100, on 01 you get hit with all negative consequences" or "roll with Advantage, if both dice are nat 1s you get hit with all negative consequences." A middle-of-the-road version is probably a natural 1 on a d20. A harsh version would step up the threshold over time, with the harshest doing so by large amounts without allowing any reduction (e.g. at first it's nat 1 only, then anything 5 or less, then anything 10 or less, anything 15 or less, and then only a crit will save you.) This is relatively harsh because it implicitly invalidates at least part of the discovered interaction, but it at least allows some amount of opportunity to benefit from the discovery.
- Finally, harshest of all, you could just rule that every negative impact that affects the simulacrum always affects the spellcaster too. This essentially soft-bans this rules interaction, since there's now no difference between having the simulacrum cast wish and doing it yourself, other than whether you spend an 8th level or 9th level spell slot...which you only get one a day of either of those. I personally don't recommend you do this, but this is pretty much the end of the line, the only more restrictive thing you could do is just outright explicitly ban a simulacrum from casting wish in the first place.
As I mentioned above, there are other possibilities for how you can deal with this, but they depend on having an invested, cooperative player who is more motivated by narrative losses and concern for the world or people in it than for pure, individual character power. If the consequences of a poorly-structured or dangerous
wish are bad enough that the player chooses not to use the power except when it's really,
really important to them, that naturally leads to limitations on exploiting it. If done well, particularly on the back of forthright and adult conversations with the player, this can also quite easily avoid any issue of feeling punitive, as an invested and cooperative player will generally understand and accept that "with great power comes great responsibility."
Well short of banning the spell or houserules it's a legit combo.
So you can fix it or not. Houserules or ban pick your poison.
These are far from the only two options. Why push it to such a false dichotomy?