I am afraid we are talking to a wall, this is Ubisoft after all. Nothing is going to change from the beta to the main game. They were just testing their "Super Duper Ghost Network" and server performance under load. That. Is. All. I dont think any of the issues mentioned below and by others will get addressed, its too late for that.
I agree with many of the points other users have posted, would like to add a couple more for Ubisoft to ignore.
Destruction. If i drive into a canvas tent with a Humvee, i bloody well expect it to fold and buckle. There is ridiculous disparity of attention to detail in this game. The roads and the surface effects like tesselation are amazing, but at the same time i cant blow up a tent? What??
Gore. There is none. We are killing people, human beings (and llamas) with high velocity rounds tearing through their bodies. Where is the blood? Are we fighting an army of drug dealing robots? When an enemy is killed there is no evidence that he was actually killed, they look clean and smooth, just sleeping. When i grab an enemy, i want the option to knock him out OR execute him in a spectacular fashion. There is nothing like that!
Hand to hand combat. Why are my silent takedowns always non-lethal? Give us a choice or make them lethal at the very least! I dont want to choke out the cholo in a dirty tank top, he murders innocent villagers and rapes their daughters. I want to cut him from ear to ear! I want to shank him repeatedly while his muffled screams fill my tactical gloves with spit! Why are tactical super-soldiers like ghosts hugging them until they fall asleep? There are no gun takedowns either. I want to use my silenced pistol in close quarter combat and takedowns Sam Fisher style, quick and deadly Krav Maga and all that.
Roleplaying capabilities. Need some kind of HQ or a jungle base. And no, i dont mean those lame "HQ" that we had in the beta, where all that makes it your HQ is the loadout crate. I want to have a remote shack in the jungle with bad quality TV, apple boxes for sitting on, a gun modifying table, some hammocks and folding beds, a half-dismantled humvee in the corner, some dirt bikes and their parts strewn around the place. Give us at least some RP fuel.
Depth. Maybe we will see some more of this in the main game, but beta felt very unpersonal. There was no reason for me and my character to care. Sure we are taking down a drug cartel that kidnaps, kills and tortures. What else is new? The characters are utterly forgettable and i see no reason to think twice about any of the goons i shoot.
Decorations and clutter draw distance. I had a strange issue with the clutter and various rubber draw distance. At one instance i was trying to snipe a guy from good 300m away, and would land every shot, but he would not even flinch. Like he did not care much for my bullets. Only when i got closer i realized i had been shooting at an invisible corrugated metal fence (which should have been penetrated by high velocity sniper rounds anyway). What was weirder, was that this fence would not just suddenly show up or materialize when i got closer. It would "grow" from the ground. It was so jarring i can hardly describe it. It was like a long range LOD sprite, that grew to its real size when i got closer.
I sure hope at least some of these hings will reach the devs ears and eyes. All we can do is hope.
TL;DR Get Sam Fisher in the office ASAP to teach and advise "Ghosts" how to conduct stealth operations and engage them in combat. And to teach the devs the meaning of lethal or non-lethal choice and the difference between them. STAT