That sounds a bit generalized and overly negative if you say it like that.
Factually yes, the MC doesn't have his/her very "own" story, but think of the format a Pokémon game offers.
The best one could do is add specialized dialogue/scenes here and there
(thinking of it, that reminds me of the support system in Fire Emblem having to be implemented in a totally linear game).
There never was a lot of "role" in Pokémon and it's a huge field to improve on in the original game series, if they want to.
You don't even get a real story for other characters. Most of them you meet once or twice, except for your rival(s).
And it's mostly like "yo I've gotten stronger this time I'm really gonna kick your butt, but politely".
Having the little underlying romance thing in OR/AS going on was already a high high for an original game so far.
May told me she worries about me a lot. And thinks of me all the time.
And that I'm her very very very best friend.
After these words, Groudon and Kyogre cringed so hard they blew up Hoenn. :>
Back to Reborn though!
Experiencing the stories of all these characters is what somehow makes Reborn Reborn, I feel.
As a reminder, just look at all these buddies:
And those aren't even all the characters (but almost).
They provide so many instances to sink your brain and emotions into.
Let's take a rather iconic scene, I heard it involves a diary or something.
Did I think the decision to tell or hide the story would have a real effect on the progression? No. (Emmeryn??)
Did I spend hours thinking about it, describing the situation to friends abstractly (since I'm gonna make them play E16)
and asking about their take on the situation before deciding? Totally YES.
Should things like these affect if other characters are hell of a lot pissed about you? I agree with you, ideally they should.
BUT:
Working through the whole game again and again to figure out the best way to influence all the relationships... whew.
It would not only be "what actions give me - or + for which characters", but also how to be -authentic- about it, leading into myriads of dialogue.
The workload seems excessive and it sounds like a last-official-release (or even a modding) phantasy.
I am not taking away from the idea itself though, it would round out the MC for sure,
and not to forget, some groundwork relationship variables will already be set with E16, iirc.
The whole region and story is filled with so much life by all these good/evil/wonderful/Fern/crazy/lovely/... characters.
There was only one game series that took a comparable toll on my emotions concerning its characters, which was Mass Effect.
I think all that we can think of to ask for are comparatively exotic icings on the cake!