i have not tested this out, so, YMMV.
starting with the same pet, IDK. it's not hard to do.
it's everything afterwards.
i believe you can get this to work if you disable the pet swapping/ratings on the advanced tab, with the "I knao whatz do wif buttons, heet mah to Proseedz in your Pets o Batizzleszs" option. (i may be contemporising the title of the GUI item.)
of course, this requires knowing what to do after this point, and also requires knowing how to set up a new pet rating system, and the conditions you would have in mind that would benefit from doing so.
from there, i *believe* you can then edit the first pet slot loaded on the first tab,
which hard-sets the pet order for the swaps. but, at the moment, the rating system works as a "empty shell" for equal level pet battles, and the rating system handles all sorts of conditions for regular battles. replacing it with ... nothing, would do as you require, but it's everything else that would be disabled in the process.
if i speculate,
it's semi-useful for PvP to put up a buff from the val'kyr, anubisath idol, crow, or something longer lasting, an aura/effect, like darkness, or a stun, different weather,
also for power-levelling pets. you'd probably want a meta-condition that ranks pets with 100% health, below level 25, as 12,300 (random high number) and then rank them as -11,000 (random low number) once they drop below 99%, forcing them to the bottom of the swap list. or treated as dead.
and, while that seems valid, what if there's 2 pets below 25, 1 level 25, and the level 25 pet dies. it would have to forfeit the fight entirely if all 3 read as dead. so, yes, it's complicated.
speculatively,
there's a possibility of adding in swap-logic, i.e. choosing how and when to swap in pets, it's very much outside the current pokehbuddy design, because
1/ it would not work like the rating system, it would have to replace the rating system or use the numeric rating system, as indicated in the example with specific switches or new variables that require situations
2/ you'd have to work out those situations ahead of time.
3/ and put code up to do things under those situations.
4/ a meta-logic like this, would have to override per-pet logic for certain odd events, like auras, weather and stun/polymorph/suicides and future random hijinks.
5/ doing so, would mean having a list of things to do with that setting, which would get more confusing than it currently is.
6/ if you think 4 to 24 lines of conditions is bad ... heh.
you'd need
a list of pets in your team (or a handful of "counters" as unique stored pets, or "counter Teams" stored for PvP)
someone to actually test these teams out and put in all the ID's and layouts for you.
a list of enemy pets, or their auras and abilities.
what they can counter,
what their main cooldown is
how to counter specific enemy abilities (by pet name)
when to swap,
what to swap to
... if you need specific pets to swap in against enemy pets
storing the current cooldown for specific enemy pets,
remembering how long an ability has a cooldown for, so you can swap in pets to "absorb" a cooldown, etc.
keeping up an aura or buff on a team by swapping in that pet or pets to keep that buff alive.
and then, storing all of that, or keeping a set of teams ... a normal team would be 1 unique pet each slot, so the number of teams is 551 x 550 x 549 ... a small number of possible options. well, mathematically.
you can also have 3 of the same pet, so the number's slightly larger, 551x551x551. if you remove the duplicate critters and so on, but add in the breed types, it goes up again. etc. my memory of grade school memory about coin tosses and probability experience/memory is rough, but i'm sure it's more like ... 650! because of the max number of pets you can have under a b.net account, and not the maximum possilbe pets. 650! is ... large.
eventually.
until it becomes a necessity for raiding or dailies or something more potentially exploitative,
it's still a hobby. and should be enjoyed or ... tolerated ... etc.
and while it's difficult to get working,
it just needs someone else, or yourself, to do the work... and therein lies the complication