I guess I don’t have a problem with constantly swapping in or out. Swapping without a SIA is inherently risky because your opponent gets in a free hit, and swapping with an SIA locks you down for a bit even if your opponent does cleanse (though it would be nice if those cleansing moves did less damage sometimes: looking at you Dracoceratops), so you have a bit of time to deal with them, and a swap-out is usually telegraphed after the cleanse.
No, the main “problems” with SIAs in my view come down to two factors:
Unpredictability. Unlike every other move in a dinos kit, players have no way of knowing when or even if their opponents is going to use one, much less which one it will be. This surprise factor is fairly unique to SIAs. The counterplay is basically to assume your opponent is going to use an SIA every time you get to low health, but there’s no guarantee that your opponent will even have an SIA, causing you to misplay and swap out when you shouldn’t.
Ultra-priority. Not only can you not predict when a SIA is coming, there’s nothing you can really do to counter one (outside of preventing the swap in the first place, which is negated by any dino with Swap prevention immunity). Even priority moves like Instant Invincibility won’t save you, when again they would work against any other move in the game.
Alone, having either of these traits would be fine. But combined they create a legion of dinos that can blindside you with secret ultra-priority moves. This is why SIAs have come to dominate the meta: all meta dinos seem to either have a strong SIA or counter swapping, sometimes both at once (like Phorurex). Of course we’re used to it by now, and there’s enough of an ecosystem built around swapping now that it (mostly) feels balanced. But we forget that any dino lacking in SIAs or anti-swap just cannot be meta relevant, pushing what would otherwise probably be completely viable picks to the side. The fact is that the swap meta doesn’t leave a place for all dinos; and since the swap meta IS the meta, this effectively excludes entire portions of the game.
So for balance, I think either the surprise element or ultra-priority need to go. For the surprise element, the only solution would be to reveal teams before the match, but that might increase drop rates since you’ll be able to tell more frequently when a match is unwinnable from the start - so that’s NOT a good idea. So if we’re leaving the unique surprise element of swap-in attacks alone, that means we have to deal with their ultra-priority. One solution would be adding new moves that specifically target swap-in dinos like @VeteranSen suggested here. It would be even better if these effects activated after a swap but before a SIA (sort of like how trap cards in Yu-Gi-Oh activate in response to another card, but the trap cards effects resolve first). That way, when your opponent does use an SIA, your dino can distract them, stun them, or put up a shield. While these moves would help counter and deter swapping strategies, their main drawback is that they don’t directly help any non-meta dinos that don’t recieve these abilities, leaving them as useless as before. So I think a more universal solution is needed.
The simple universal solution is to give SIAs the same priority as other moves. That way any faster or higher priority move can counter them. Trying to use Swap in Stunning Strike? Too bad, I used Instant Invincibility Taunt. Or my cunning just used Distracting impact against your slower resilient - forcing swappers to spend their boosts a bit more evenly, since currently all they really need is enough health to survive until they can swap out and maybe pour the rest into attack.This instantly would give tons of currently off-meta dinos options to counter SIAs. But not all SIAs are really problematic, and some like Swap In Distraction and Swap In Invincibility need their priority to function. For those moves, they would be granted the same level of priority as stuff like Instant Invincibility - so really, only damaging and rending SIAs would have normal priority.
In exchange for this general nerf against swapping, they deserve a quality of life buff, and that would be letting you choose which dino you swap to after an automatic swap move instead of it just being the next dino in line. That way, swapping strategies that use these moves are less dependent on the RNG of drawing your team in the right order. Honestly I think this change should be in the game already, but swapping is currently too strong to justify a buff like that, even if it makes the game better to be. In the context of the general swapping nerf I suggested, this buff would be far more justified.