Why would you Shove without a follow-up?
Knocking someone down is not really a good strategy in any fight (real or imagined) if you don't have a follow-up. When was the last time you saw a UFC/MMA fighter push someone to the ground and then just let them get up? When somebody in a gang does a shove, they're doing so to let their friends jump on the fallen.
Once you knock someone down, your next step is really to Grapple them or attack them while they are on the ground. A Grappled creature's movement is reduced to zero, so you can effectively prevent them from getting up (like the gang above)
In fact, the Monk actually do this Shove and Attack starting at level one with their Martial Arts skill. So you knock somebody down (Attack Action), kick them in the head (Bonus Action) and even step away if you want (Move Action, their AoO at Disadvantage). If you move away, they typically can't attack you on the following round because they have to waste their movement standing up.
Note that at 5th level a Monk (or other PC with Extra Attack) could do both a Shove and Grapple as part of the Attack Action to effectively pin their opponent. Escaping the Grapple requires an action and standing requires half movement, so pulling this off pretty much wrecks the target's turn.
This is clearly a gang-up tactic, but that's expected.
Is Initiative the Problem?
Consider that the problem here may actually be the initiative order itself.
You point out the problem of effectively "metagaming" the timing of the action, but also the problem that it will basically never allows you to benefit.
DMG (P.270-1) presents an alternate initiative system titled Speed Factor.
Under this variant, the participants in a battle roll initiative each round. Before rolling each character must choose an action...
This is followed by some modifiers for speed and action type. The action order in each round is random (weighted). This means that knocking someone prone will always have at least a chance of being useful. And there's no "house-ruling" required as this is straight from the book.
If you're really worried about the metagaming aspect of Shoving/Grappling etc. this might help as well. I've used this "initiative per round" and it does kind of solves the problem of gaming the initiative order, both for things like Shoving and for things like Healing. However, it introduces other problems like wasted Actions. So it may be a little much just to solve the Shoving problem.
The Elementalist Fighter class is more powerful at every level than a standard Battlemaster Fighter.
I'm using the Battlemaster Archetype as a reference point as the OP has stated that it is an influence on the homebrew class design and because the class features closely mirror that of the Battlemaster.
TLDR; Elementalist Fighter blends almost all of the features of a Battlemaster, adds a sprinkle of Barbarian and then adds a tonne of powerful abilities to boot.
- Second Wind comes 2 levels later, decreasing survivability at 1st and 2nd level, before returning to the status quo at 3rd.
- Weapon Bond is almost identical to the Eldritch Knight feature and comes 2 levels early. It somewhat undermines one of the EK's unique features but is not too major.
- Imbue Weapon is a reskinned Barbarian Rage, the quintessential Barbarian feature. It is more offensive focused than defensive. There doesn't appear to be an end condition, but I'll assume it's the same as Rage. Almost everything here feels out of flavour for an elemental focused fighter. Psychic resistance, temporary darkvision, changing the advantage on checks and saves to Charisma, and advantage on saves against being charmed are not, in my opinion, things I would associate with a class called "Elementalist Fighter". Mechanically, choosing the additional damage's type is strong as it somewhat enables low-level melee fighters to circumvent physical damage resistances, one of their greatest banes. It is somewhat comparable to the 3rd level Elemental Weapon spell, minus the to hit bonus and magical weapon consideration. Losing the physical damage resistance of Rage is not a suitable drawback, as Fighters are much more capable of achieving high ACs at low levels than Barbarians, through heavy armour, shields, and fighting styles. So the loss of defensive abilities is negated by the classes intrinsic high AC and the damage capabilities are greater than the standard Rage, with some odd extras thrown in.
- Maneuvers. Having extra restrictions on maneuvers is sure to only cause confusion. The save DC being Charisma based is also quite unexpected and again outside of the classes flavour. Some of the new maneuvers are far above the current power level. Elemental Slam stands out as particularly egregious. Fighters lack AoE as a balance requirement. Giving them access to AoE which does good damage for a relatively low resource cost, is definitely going to cause them to be overpowered relative to another fighter of the same level. In conjunction with the powerful secondary abilities that many of the damage type Slams offer, I don't know why you wouldn't pick this maneuver over any other.
- Ancient Blade doesn't have any real balance concerns. It does, however, cause a great deal more work for your DM, which is something that I would consider poor design. Know your Enemy of the Battlemaster is pretty whatever, but it doesn't cause any additional preparation or forethought that could be used on the game as a whole, instead of one character.
- Elemental Incarnation is absolutely insane. Indomitable is already a strong class feature, and EI blows it out of the water. It evaluates to casting one of the Investitures of X spells, without the need for concentration, once per day, at the cost of one level of exhaustion. And this is in a non-casting class, 2 levels earlier than a full caster could. The sheer damage output and/or utility that this feature could provide in its 10 minutes is incredible. Especially considering most conditions that require a save also give one each turn. Potentially missing a turn or two is well worth this.
- Elemental Explosion is again powerful because it gives Fighters access to powerful AoE at a relatively low cost.
If given the choice to play a Battlemaster or an Elementalist Fighter, the Elementalist is the clear winner. With its access to cheap AoE and additional damage output, it does everything a Battlemaster does and more. It suffers from a lack of identity, borrowing iconic features from other classes, and also having a mix of features that don't resound with the classes core concept.
Best Answer
Crouching is a no-brainer
And no-brainers are bad design --- you've created a new action that has a very negligible downside. No wonder your players are spamming it!
Think about it --- the only downside is moving slower, but the character can stand up for free, so that downside hardly ever comes into play if the player uses the rule to its fullest.
I would honestly recommend dropping the rule, since it overlaps with the already existing actions Dodge and Drop prone, and by what you describe it's not really adding anything but new rotes to your game. Crouching, bending, swaying and such to avoid ranged attacks is also something abstracted in the characters' AC.
But if you really want to fix it...
Disadvantage is too much for crouching. It's like dropping prone without any of the downsides. Also, the action needs to have a cost or condition to not be spammed in every possible situation. A mere "tweak" won't fix this, so if you really want to keep crouching in your game I propose this instead:
Making it cost one's bonus action introduces a reason not to do it, and restricting its use to places where cover is available makes sense in two ways. First, it reduces the potential for spamming this action. You can also explain that one needs to have a source of cover for the "reduced size" to significantly outweigh the defensive effect of having harder time moving.