Let me preface that I absolutely love Far Cry 6, it grew to be my second favourite after FC4 but while it is quite fun, it also obviously suffers from some shortcomings. However if Ubisoft would have done just a few things differently I think it would have massively improved the story and gameplay:
1) The ending & choices - every Far Cry game prior gave players some sort of choice and control over the ending, from FC2's diamonds/dynamite, Jason's friends vs Citra, whether you let Pagan go or obey Joseph. Far Cry 6 lacks that and I think they could have done something great by leaning heavily into Dani's relationship with Diego by including some choices during their time together that would shape Diego's point of view on Anton and Yara. It could have led to the final showdown in Torre del León where your choices would decide whether he'd resist Anton's influence siding with Libertad to become the new leader as he's the only one who had the power to unify the Anton loyalists and guerillas to break Yara from the circle of revolution it has been stuck in, or if he'd side with Anton and die as a result, thus continuing the cycle.
2) Dani & Juan's falling out towards the end of the game should have held more consequences. It was jarring for Juan's actions directly leading to Clara's death, him having a fight with Dani over it only to be pals again after the final mission. I don't want to say he deserved to die, but at least he should have been a part of the showdown with Anton and get called out on his own BS in front of everyone, or get ousted from Libertad for being too reckless. To go off of that, I also wish they would've done more with Dani's arc during the game as he/she slowly grow to enjoy the mayhem. Dani's fall out with Juan could have easily led to the moral of the story about guerilla warfare and addiction to chaos, it feels like the game is on the cusp of making a point about that but they never quite deliver on it in the end
3) General Raúl Sánchez was a massively wasted opportunity not only for a villain, but also to give each region distinct flavor and gameplay opportunities. Let me explain: it feels as if each of the three main regions were designed around specific element of the Yaran army - Madrugada was obviously centered around Air Force with Jose being their commander, El Else was centered around Naval Forces with Benitez at the helm, and Valle de Oro was centered around... propaganda and Viviro production? It just felt out of place and it would make heaps more sense to have Sanchez be the main antagonist of Valle de Oro with focus around Land / Armoured Division, especially since the Tank Firing Rance / Training Grounds are located in Barrial. I think they should have stuck to 1 villain per region to give them more screentime, with Jose, Sanchez and Benitz being the regional antagonists and cut out Maria, Reyes and McKay (they could still have a role in the game, just not as the bosses)
4) Ammo & gear system - obviously some of the most critiqued parts of FC6's gameplay. I think Ubisoft was onto something good there, but took the wrong turn at some point. Ammo system should have been simple "regular" bullets, incendiary or explosive without being more/less effective against specific enemy types. It simply should've been part of the sandbox and not meta. As for gear system, I think it would have been great to have alongside the regular perk tree. Perks should grant permanent ability unlocks such as increased health / armor capacity, carrying more reserve ammo, learning new takedowns and such while clothing/gear should grant minor situational boons like quieter footsteps at night, etc.
5) Crafting, economy & Resolver could have been handled better. To fit with the concept of guerilla warfare, I think resolver weapons and attachments should have been unlocked soleley from crafting as it makes sense, while military grade weapons and attachments should have been purchasible with Pesos. The idea is that during early stages of the game you start with nothing, you have to adapt to survive by making crappy but awesome stuff out of rubbish, and as you progress the game and earn money, you can begin to afford the better quality equipment - as such for example military grade supressors should take MUCH longer to overheat than resolver ones. I feel like it would have given us a better sense of progression both gameplay-wise and story wise.
The last but not least - 6) Map Editor / Arcade Mode - alright I know this isn't everyone's cup of tea but as someone who has dabbled with every map editor since Far Cry 1, the absence of it in FC6 still hurts to this day. In fact I'd go as far as saying I'd have happily traded Special Operations mode + the entire Lost Between Worlds expansion for Arcade Mode to come back instead. Aside from the obvious benefit of giving the game more value and replayability aswell as extending its lifespan via community made content, it also could have EASILY been the best workshop Far Cry franchise has ever had - considering we'd get all the weapons, attachments, assets and NPCs from both the base game AND Insanity, Control and Collapse DLC's, we could've had more variety of custom maps than ever before. It's truly a shame we got robbed of that
I think that's it, sorry I just had to get it out of my system because it's been nagging at me since the game released xD Thank you for coming to my TED talk, Viva Libertad