LoverIan's Suggestions

Second, on the deal of Selkamater, I've got an idea. I love the theme of radiation used in this, and it would be useful to suggest that levels of radiation have made Selkamater MUCH more rare than it is hypothesized to have been. Human hunting and other interactions did reduce levels, and the radiation leaks have only made numbers so low, Selkamater is considered endangered.

Your mission in Anthell is not only to rescue your friend, but for conservation itself!
Selkamater must be fought, and not caught. This is because the royal jelly must be harvested from her when fainted, as an awake Selkamater never gives up it's royal jelly willingly, and it is found within the Selkamater's body.
A Selkamater is not normally made until a queendom can be secured, or the reigning Selkamater perishes. Currently their instincts say no area is safe aside from their Queendom, sensing the radiation in nearby areas. Smore, Sponee, and Tricwe are hardy enough species to survive elsewhere, but they and their evolutions refuse to let their Queen leave, and thusly wouldn't let another Selkamater leave.

Selkamater is defeated, the day is saved, everyone goes YAY, but the situation immediately changes. It seems that Anthell was more compromised than Rangers let the locals believe, and you.
If implimented in game, a hoard battle begins. Or a triple battle. A radioactive Smore, Sponee, and Tricwee attack, and Tiko assists you.
Once defeated, Selkamater arises from fainting, in a radioactive, and more powerful form.
I'm not sure the radioactive mechanics, but giving Selkamater's radioactive form an ability that makes it's attacks all radioactive, and giving it either giga impact or hyperbeam, would make it a true threat in battle.

Once defeated, and this time gone for good, the hive threatens to collapse, and a few Rangers bust in, or Tiko assists you in harvesting royal jelly to help in conservation efforts.

You get some Royal Jelly, Tiko gains a Selkamater.
By the time you get to the Elite 4, 3 or so new Anthells are being made, and by the time post game begins, you can visit those Anthells, which are the size of a 2 story building, due to how fast they build.
You can also visit Tiko once a day, or maybe week, after, to get some Royal Jelly. Tiko regrets the collapse of Anthell, and having to medicate her Selkamater so that the species may continue. Only by having one in captivity able to be studied were they able to find a method to harvest Royal Jelly.
Lastly, in the name of post game, and the whole pirates versus ninjas, maybe the factions in the region are attempting to raid the Anthells for royal jelly, so that they can have overpowered armies?

I know it may be a bit crazy sounding, but it could be a compromise, Selkamater can't be caught due to radioactivity, and the evolution method can still occur. I also devised it because I personally see it as the type of pokemon that would try to make hives in several places in the region, and a way to show how destructive the radiation has been.

The original berries from the games can be used, but those berries could be used for much more. For example the Acai Berry could be used to make a Radioactive Attack hit as if it were not supereffective. Additionally, Acai could always cure all status conditions, and maybe even heal the pokemon a little. Now what is bad about this miracle berry? It's rare, and people fight for it, but what nobody notices, a few turns later cause damage to the pokemon having used the Acai berry, with no explanation, as if it's bad luck. The only person in the region to say what it really does to you is someone outside a health store saying "Yeah, it may seem great and a ton of people may be buying it, but it has a delayed affect of harming any pokemon to eat it, it causes a dependency."
Guara Berry? Why not make it make a pokemon's next hit supereffective, but only when they've lost up to 2/3 or so hp, unless they are a glutton. The other option is upon being hit by a supereffective move, the speed essentially doubles or so.
Cupu and Bacchu could do the same, but instead....
Bacchu when eaten creates a strong scent in the air, or when used. If a pokemon is at the lead of a party after a Bacchu berry is used on it, it drives the encounter rate wild. This is inspired by seeing the only thing coming up on google for bacchu berry as a similar spelling but used for fish bait.
Cupu berry could be used to drive the encounter rate down, but to make things interesting, it's a correlation. If the Bacchu berry drives up encounter rate, why not drag down level, and for Cupu, why not drive up level.