I think you're overestimating the Mako's popularity - plenty of people have expressed dislike towards it, at least based on their experiences of ME1.
And you may be overestimating the extent to which people dislike the Mako.
The only complaint I've ever heard about it was that it's handling is scittish, which I found only to be true when you were driving recklessly over ragged terrain or trying to jump over mountains. Barring that one Prothean site on Eletania for the trinket quest, every point of interest on ME1 maps can be accessed from easily recognizable paths if people just looked at their map and have rudimentary knowledge on how to understand elevation mapping.
My personal experience with the Mako is that it handled perfectly fine for as long as you weren't deadset on going in a straight line from A to B, no matter the terrain.
That having been said, I don't particularily mind if any potential planetary exploration in ME:A could also be handled by a hovercraft like say the Hammerhead, for as long as the vehicle isn't made of cardboard like the one in ME2 and the map design facilitates a sense of exploration as opposed to just speeding around. That part was actually handled pretty well in ME2 Overlord with the locale being on a grander imagery scale so even when you were blitzing around, the massive cliffsides, caverns, mountains and massive long distance drawing of backgrounds and the skybox still gave the impression that you are but a small thing in a big world, but if you want to apply that on a larger scale for several big planet maps as an integral part of a game and not just part of a DLC sidequest, then that's a lot of work you're suddenly looking at, both for the developers to produce aswell as for any machine to render when you play it.
As such, I believe having a wheeled vehicle with its more grounded gameplay (pun intended) is more economic to work with for the developers. If you can speed around like with the Hammerhead, the sense of exploration is more about the grandeur of the location, whereas a more paced (pun intended, again) travel can emphasize the journey as an integral part of the explorative sense (which I'd also prefer, personally).
Now, the exploration aspect aside and moving to the other gameplay component - combat:
What kind of gameplay does the dev-team want to use in ME:A for vehicular combat (if they even want this to be a thing) ? Should it be fastpaced version with you rocketing around dodging missiles, chase scenes and whatnot, or is it going to be slower, more heavy like driving around in a tank and cumbersomely, but surely clobbering your way forward as you plow forwards?
Knowing that the developers have/want a combat system very similar to ME3 (which is good, because the combat system is solid (if only they'd improve the enemy spawning system and make it more intuitive instead of having Cerberus troopers suddenly jump-pack from nowhere behind you and *blam* shot in the back) which is of the more fastpaced nature, I think vehicular combat could do well to contrast and be a bit slower.
And who knows, just because we get the Mako back doesn't mean there isn't going to be a shuttle you might fly through ragged valleys or asteroid fields in a space-fight chase/escape scene to give players a fastpaced vehicular gameplay experience.