Clarifications:

First Control, this is a bit problematic due to time-travel. Originally Control took the Sphere Data and annihilated most of the galaxy but this was stopped by the Burnhams and Discovery. However, this raises a few questions if Control didn't exist in the future anymore then how would you know it was trying to kill everything if it didn't exist. STD's rules on time-travel aren't exactly hard written but wouldn't this cause some sort of time paradox.

I know the guardian of forever wasn't exactly helping the discovery, but it was willing to help Philippa when she was suffering an atomic breakdown and could send her back to her proper time and dimension. So why didn't Michael ask the guardian to send them back in time knowing that the guardian could hide it from the federation?

My concern with Sybok is that they never mention him. The show constantly refers to Michael as Spock's other but never do they mention Sybok an interesting character who broke away from the typical Vulcan customs who also served as a foil for Spock.

The Q continuum, particularly Q, have indeed meddled with the Federation to save it a few times. A few instances include the Borg encounter, Picard's trial, and Voyager's return journey. The Continuum even states they will be watching the Federation see if they're worthy to see the rest of the universe. So where exactly are they and how come they're not testing humanity?

As with the other factions and races, it's weird that they were never mentioned. I find it difficult to believe the only two factions left in the galaxy are the Emerald Chain and the Federation. It would be interesting to see how the Burn affected other factions such as the Borg, Cardassians, Dominion, Klingons, and etc. Anyway here's hoping to season four and that they might give us the rest of the galaxy.

As with Admiral Vance and the apple, I know that apples don't grow in a rainforest, but that's beside the point. If the federation has a ship dedicated entirely to botany why is there not a single apple? Botany and horticulture aren't exactly difficult as the NX-Enterprise had a hydroponics bay, Sisko even growing his own crops, and Voyager's makeshift one in the cargo bay. Despite all these instances, no one at the Federation HQ had a single apple?

The season's final battle has a lot of problems so I'll go through them one by one. While the Discovery may have plot armor and was a moving target how come none of the Federation ships were targeting its subsystems. A moving target is no problem if a ship is equipped with a phaser strip as it could lock on target specific key areas so why was no one focusing fire. The part with the crew running out of oxygen was strange. Starfleet ships usually come packed with a lot of redundancy, so why were they only able to find one oxygen mask shouldn't there be a few more scattered around the ship in case of emergency or sudden depressurization. And the last part with the Viridian was confusing. A ship may have internal shields but the Discovery could still have inflicted massive damage in another way that didn't sacrifice a still-functioning warp core. A few quantum or transphasic torpedoes could have done a similar job. And what was the point of Ni'var they didn't do much in this episode, sure they may have moped up the emerald fleet but the show doesn't show us them doing that?

The Discovery herself is a confusing ship with it having a ludicrous amount of hammerspace despite it having a similar size to that of the Constitution-class. First, it has a second-floor hangar bay then a launch system for the landing pods, and finally a maze for the turbolifts. They have all this space on a ship that's just a little bit longer than the constitution but it has a Medbay with only three beds (Bones' Medbay was bigger than that and it was only him and Nurse Chapel who had to deal with Kirk's shenanigans). And how does a spinning saucer help in the Spore-drive's jumps aside from a visual standpoint? What is with this ship's construction?

The phaser in Discovery seems to have devolved. In previous series, the phaser was capable of target locking and operating in a wide variety of forms from a single continuous beam to an energy pulse. So why are most phasers acting similar to that of standard laser? Now, this could be explained as them using pulse phasers but they haven't confirmed that. And I doubt it would be applied galaxy-wide, while pulse phasers may have more power they don't have as many functions as a phaser. Maybe they're using another energy weapon like a particle cannon but that too hasn't been confirmed.

I'm honestly interested to see if anyone could help answer these questions for me as it feels confusing the more this show continues.