Why are there still wheels and land vehicles?

I can still see wheels being practical, to be honest.

The higher tech something is, the easier it is to break it. Wheels are going to be much more reliable than hover tech, especially for a vehicle out on the frontier.

Plus, the Mako has no time for your physics anyway. It's not like terrain has ever stopped it(which would be the main benefit of using hover tech is ignoring terrain).

Yeah, it makes little sense to have a wheeled vehicle in the ME universe, but hey... you don't get to enjoy tearing up all the cool, Frostbite-driven landscape flying 30,000 feet above it.

Energy consumption, viability in different gravity environments, lower emissions, better stealth capability and the capability to house a cocktail bar make a wheeled vehicle an excellent pick for intergalactic expeditions.

To be blunt: shitty lore bad world building, possibly combined with the fact that they had no idea how to handle the alternative but wanted planetary exploration anyway.

Consider the lore of Mass Effect's guns: weapons that shave ammo off of a super-dense block of base material and compensate the weight of that block with an integrated mass effect field, only to arrive at about the same weapon performance as our comparatively utterly primitive present day weaponry. Despite the fact that the ammo you load into Mass Effect's weapon is supposedly a "thermal clip" that acts as a heat sink, pretty much every weapon's "rounds per thermal clip" is inspired by present day ammo capacities and not by the potential heat generation of the weapon as it should be. Single shot standard pistols should have a nearly unlimited ammo count if the limitation were the thermal clip, because pistols fire low velocity rounds that cause little heat. Who has ever managed to overheat a present day pistol? Machine guns, on the other hand, should either require several thermal clips (which they don't) or have a very low "rounds per thermal clip" count, because these things generate a lot of heat, wearing out a clip that much faster.

Also, I should be able to freely decide for which weapons I want to use my thermal clips since they are supposedly universal, but picking one up just increases the spare ammo count of all guns carried, so I'm somehow forced to split them. Finally, despite the mass effect field that counters the weight of the ammo block, weapon weight still exists as a balancing factor in the game. Why the hell do ultra light materials exist if, according to the lore, there is a mass effect field to reduce weight? You could just adjust the gun's weight to something a given soldier is comfortable with.

And this is the lore for guns, a mass produced item that every soldier requires. Overengineered as all hell, as far as the lore goes, for no measurable gain in efficiency over present day weapon designs, plus some nonsensical oversights as a bonus.

And then we have the Mako. A single piece of technology attached to an exploration vessel. Given the weight reducing mass effect technology being mass produced for guns as described above, this should be a flight capable hover vehicle. An armed, flight capable hover vehicle, given that we're going off into the unknown. Instead we get an unarmed truck. Maybe they just don't know how to implement a proper exploration vehicle, and the code for wheeled vehicles came free from DICE.

The armor on the alien races.... they can go nuts on the new designs. But don't touch Ryder's armor, I swear to the Maker.

Not that I disagree with you, but it seems for your post that the Mako problem came with Andromeda, while the lore of Mass Effect, as wrong as it can be, have wheeled vehicles from the start, and the Andromeda expedictions seem to be based on the same technology of the former trilogy.
They could've gone with developing the new vehicle based on the Hammerhead And not the Mako, but I think that the choice was more based on the former being even less well received then the latter.
I do agree with the weight system, though it existed since the first game. At least with ME3 you can decide which type of weapon pick. 

 

It makes sense to me that an armoured combat vehicle, like the ME1 Mako, might not fly/hover. I mean, you could probably make a hovering version, but if you have to compromise armour or weapons systems to do it it might not be worth it.

Mass Effect technology doesn't make weight irrelevant, you need more power and a bigger core to counter bigger weights.

The ME3's apparent light scout Mako seems odder, though. I don't really see why we don't just take a shuttle

That's true. I hope they change their minds and add weapons to the Mako.

While I agree with you on guns, I've always thought that hover-tanks while looking cool are a ridiculous concept.
If you can make a hover-tank, just make a flying tank instead. Besides engineers always tried to slap on a tank as much armor as possible, if it still can fly you clearly haven't put enough armor on it

Do you mean hover tanks in general or in the Mass Effect universe? If you are referring to the Mass Effect universe, then yes, you might as well make the vehicle fly all the time unless you introduced some "balancing factors" like an overall energy consumption rate that, for example, goes up significantly if the vehicle is flying and thus leaving less energy to distribute to shields and energy based guns. Other than that... yeah, it might as well just fly.

Although now I wonder that if a massive, non-aerodynamic object without wings had its mass reduced (that's what the ME fields do, right?) enough to fly, how would it react to a gust of wind?

Indeed, hoverbikes, even better 

Hovercraft don't work well on airless planets.