I will try to keep this ordered as properly as possible but do note there are a lot of different aspects to manage.

Base upgrade system:

Let's be blunt. It needs a complete revamp. so let's go along the list of the main offenses.

-First of all, 4 mechs on the field is mandatory. You could remove that being an upgrade to have the 4 mech capacity be the default option. Everyone beelines for this, because playing with less than a max capacity squad is something one would only do as a challenge.

-The costs of the upgrades are high, and it's extremely painful some upgrades are in fact side grades, coming with a huge trade-off that makes those upgrades something players will delay for as long as possible taking others upgrades first or only pay for them when they can also pay for something that will mitigate the tradeoff.
In general it is considered bad form to have an upgrade tree where stuff you purchase at high cost isn't a straight upgrade and/or something opening new strategic abilities. Side grades can be good for gear, but for an upgrade tree, it's not. It's just bad design. It's especially bad as it's something you can't turn off when purchased and activate only when you need it. To put it simply, to make players purchase a new door with a spikey knob that will hurt them when they use it. Don't do that.

-Upgrades to augment the amount of salvage and/or decrease the amount of salvage points needed for some operations would be great, especially early on.

World Map:

-When plotting a course, it's a good idea to not unpause the game. This makes plotting courses very annoying as as soon as you click anywhere, the timer will resume.

-Automatically pause the game when the base stops/reaches its destination. If the player wants to resume the game, and not move, they can click on the buttons to pass time. This allows greater comfort when playing instead of having the player forced to have the cursor over pause at any moment when arriving at destination. In general, you don't want to create situation auntomatically unpausing the game when there are patrols around the player is supposed to dodge.

-Tell players that boosted speed doesn't allow them to interact with missions and they need to be in cruise speed to do so... Or alternatively, make missions interactible no matter what the speed/mode is.

-Tell the players they will be placed automatically in a dangerous defence mission if engaging a patrol. Seriously, a lot of new players get caught seeing a small patrol, thinking they will attack it, and realise they are in a mission where they have to deal with protecting the crawler which somehow got damaged from constant missile bombardment or drones, while fighting constant enemy reinforcements which don't match the strength of the patrol. Basically if you want players to dodge patrols, tell them that.

-Don't force a scripted mission on the players such as "Go back to ressuply at the most distant supply point" when they have done so at the closest one.

Combat UI:

-Allows players to see if the part of their attack OUT of the 5 seconds window will lead to an overheat. Due to how the UI is made, there is no way to see that, despite the fact it's absolutely critical to planning. I can't see the overheat alert if it's out of my interface. Alternatively display a demand of confirmation when pressing execute if any mech is about to overheat, even if it's after the 5 seconds window.

-Allow a function to switch the target of an attack without having to completely delete the attack.

-Allow a function to change the destination of a move, without having to fully delete the move.

-A system of small red cursors over the timeline to indicate when an unit will come under attack in addition the the lines on the map would be extremely useful to better plan the timing of actions such as shielding and dashing.

-Make critical mission building targetteable and display their HP. Any generator should be clearly displayed on the map and targetteable. Same for any com tower calling for reinforcement, or every single building in demolition missions. It can be deifficult visually to determine if something can still be hurt, or if it's really damaged to destruction status.

-Make the dash radius closest to the ground level, or sticking to it, so it's easier for the player to know where they can, and can't dash. It's frustrating to go pixel hunting every time a dash is made because the perspective of the radius isn't really good, and don't play ball with the camera view.

-Don't auto-imput orders for Home Guard units if they are under player command. Most of those orders are stupid, and the player has a tactic in mind that rely on deciding what the Home Guard units will do.

-Display a demand of confirmation when a move will lead to a collision, to make sure the player knows the collision is going to happen. The small yellow dome is easy to miss.

Mech customisation UI:

-Allow to check the modules of non-equipped pieces. I want to see what that non-equipped arm module is, and what it does precisely.

-Allow to remove the modules of non equipped pieces.

-You may want to change the confirmation on a long press, and double click, to something safer like left click to select, right click to equip. This will allow your interface a better capacity to inspect the elements(by selecting them) without equiping them by mistake. In general long presses for confirmation is considered a bad system that most people don't like. A lot of game studios are trying to push that, and players are unanimously pushing back. Whoever is trying to teach devs long presses are a good system is wrong, and shouldn't be listened. Even for controller support it doesn't make sense: Controllers have enough buttons nowdays to not being imput-tied and require long presses.

-A way to display the stats of a piece without its removable boosters would also be very appreciated. It allows to judge the value of a piece by itself, or at least, by itself with its locked modules.

-Display if a weapon is a two hander, or locked to primary weapon slot clearly.

-Clearly explain if -XX% to mass or +XX% to integrity affect the part itself, or the whole mech. This makes a HUGE difference, and it's currently not clear.

Tweaks and balance:

-Light mechs should have a way better heat dissipation. This is pretty much what they are here for, as well as in built thrusters with the best thrust efficiency.

-Heavy mechs shouldn't be able to rely entirely on thrusters to move around, completely disregarding their masses. A heavier mech should require more energy to thrust around depending of its mass, so we don't have heavy mechs which are the Incredible Flying Building. In addition, they should only be able to thrust horizontally mostly, and very little vertically. Comparatively, they should be able to go through buildings and have a charge/ram attack which build up before propelling the mech horizontally on a decent distance. Basically, heavy mechs should look and feel like heavy mechs, and not beat mediums or lights on movement by heat dissipation and constant thrusting alone.

-Consider trying to avoid concussion damage being king of the battlefield for salvaging purposes. It leads to an unfortunate meta which discourage the use of others weapons, and what I would call the "Battlemech Marauder Effect". If you know, you know. And seing the similitudes between the two games, I know you know.

-Reconsider base upgrade costs after having revamped the base upgrade system completely.

Suggestions for the future:

-Behemoths. Yes, I know they got mostly discontinued, but I want one. That's the kind of mech which makes you feel like you are getting serious. Not only that but they aren't humanoid and show more personnality than the catalogue of regular mechs.

-Bigger squad sizes. I feel like 4 is limitating and while mods allow for more, I think it should be a feature. While technically the Home Guard allows that, it's not really the same thing. 4 squadmates don't really allow the same degree of squad composition and tactics as 6. 6 allows you to have 2 flankers, 1 sniper, 1 missile platform, 1 heavy and 1 line mech, for example. Take XCOM for example and you realise that the game only really opens and expands when you get more than 4 squadmates.

-A more living battlefield. The Home Guard as it is now is invisible until it suddenly manifests itself. It would be tremendously better if the Home Guard was visible on the map and conducting its own operations on their side, like taking out patrols, attacking objectives, retreating, ressuplying, patrolling, supporting, etc... It would allow the player to help them or make use of their presence in creative ways to ease their task. It would be nice too if hitting objectives had a more noticeable effect on the battlefield: Cutting the supply lines weakening patrols would be nice, disabling communications to make their blind at least for a time too. Destroying a base would force them to relocate to an other base changing their routes.... That kind of thing is important and makes the players feel their actions have more of an impact.

That's all I have from the top of my head.