You are talking about human adversaries, we are playing against AI so unless they can read what move you are about to use AI are pretty limited in their actions, but anyways the dev has spoken and we will have pokemon catching.
I know you are not hired only to procreate with pokemon, but you are hired to test Allerita and the Professor also mentions that you can use the gyms and the elite four as a medium to test her possibilities so I'm not against there being an elite four and gyms, but the idea of using non fuckable pokemon to beat the game goes a bit against your job, but if you want to do it go ahead.
So you understand the assignment, but still aren't satisfied with the reasoning? Its simple really. All waifumons aside from Allerita are optional. That being said, you can also bench Allerita entirely and proceed through many portions of the game without her. So far, there is only one story-based event that requires you to have Allerita on your party, because she's the only waifumon that has narrative importance to the game.
So since I cannot control who the player uses and how they build their party, it also wouldnt make any sense to have the game only center around catching and using Waifumon. As Blubbervink stated, as a researcher, your job isn't only to raise Allerita and test her capabilities, but also to explore the region and catalogue what you see. Yes, Wormwood doesn't put much importance into it, nor does he particularly care that you do it or not since his goals are not the same, but its part of your resume as a Field Researcher, and exploring the region is CORE to finding waifumon in the first place. Everything ties together eventually.
Regarding battle AI, its not as simplistic as you think. True, for the most part (especially ordinary trainers) we let the AI do what it wants. Sometimes, it does very well, sometimes its stupid as all hell. But in later portions of the game (and certain compulsory battles) I have adjusted the fights myself by rigging the AI in a sense. Forcing limitations on movepools, changing Abilities, etc to make the AI behave differently than simple "hit with super-effective moves." We implement setup, field hazards, and stat changes to give players more of a challenge. If you find the game easy, good. But the goal was never to make it so difficult that even competitive players will struggle, it was simply to make it hard enough that mainstream players will actually have to think instead of only relying on sweeper setups.
A good example of this are with the type of waifumons provided and how enemy teams are setup. In the beginning of the game, I force players to learn to setup, providing both Allerita and Lopunny (the earliest waifus you can get) with powerful combos that require stat boosting for the highest damage (or in Allerita's case, defense for sustain fights, with Destabilize as a counterweight to turn the tables).
Gardevoir is then introduced, and now players are made aware of using status effects like sleep, to help with Setup for either herself or other mons. Viruark is similar in many ways, but she now comes with the ability to set up multiple status problems and punish opponents for being too aggresive with Baneful bunker. Then you get Tsarevniya, teaching players that Defense can be a better offense and teaching players about longer-winded battles and knowing when to use her ability to negate fire attacks by switching in and out at the right moments. Drakaiden introduces weather effects and how to use it to your fullest advantage, as well as dual-type attacks.
My point is, everything, including combat evolves at a pace, and the enemies are scripted to behave differently to test the player's build. For example, the Stat-boosting tactic will not work against Novus, since 2 of her primary mons have Unaware and ignore your boosts while being sustained tanks, and requires players to think differently. TLDR; its not always as easy you might think. If you're lucky, the AI will fuck up and give you an easy win. But my beta testers and I have gone through each important matchup multiple times and can testify that when the AI does do what it should, the game is far more challenging.