The aliens in Independence day(and from what I hear they aren't much smarter in the sequal) are actually not that intelligent, nore advanced. Firstly, sure they can build the big super structure ship that I imagine a hyper advanced civilization could, but they have failings in advanced targetting computers and proper seige weaponry for pounding a planet from the stars. They had to, in the first movie, come up with an over-elaborate plan of coordinating massive space ships down to earth in the hopes the humans would be stupid enough to not recognize that as an invasion force and they target CIVILIAN centers, rather than military complexes. If they were to wipe out humanity, there are easier ways to do so:
For those interested only in resources to mine:
Death Star could blow planets apart from a few orbits away.
Episode VII takes it to an extreme with....I won't say.
In master of orion 2 you have monstrocities such as this:
https://www.youtube.com/watch?v=6e5HtWdh_rwBasically, the ship has "Achilles targeting system" combined with a few other modifications to enable it to wipe out whole swaths of similarly massive death stars. This combination works on ships of any size, although the phase cloaking device and time warp facilitator was nerfed to no longer work together to allow such a near flawless victory.(In fact, the player used armor piercing, he didn't even need that with the Achilles system, it makes ALL beam weapons bypass armor flawlessly). And of course, planet destroying beams.
In Master of Orion 3(not the best one, in fact everyone knows it's terrible), ship targeting and range can get well across half or more of a full star system.
Both games allow for construction of such super ships in very little time, to. Whole armadas of death-star sized space craft are nothing unusual.
Now now, the planet is blown up, we cannot use- oh wait the resources are just in pure form easy to mine and harvest. Unless the aliens needed a livable breathable atmosphere for resources, and if that is the case, they also failed to develop important ecological technologies(which I guess was there only reason to not use such powerful weapons). Even then though, they could simply fire a large projectile, or a few, into the planets oceans to wipe out most city life through flooding, and subsequent bombardments wouldn't permanently damage a livable atmosphere as severely as you'd think if you do not use weapons which leave any kind of radioactive residues or simply use orbital bombs with advanced precision targeting. Dropped or launched from such high orbit humans wouldn't be able to retaliate or even see whats destroying them.
Scanning technology likewise exists in the hands of humans to detect deep deposits of oils ect. So why couldn't the aliens have such technologies combined with advanced precision targeting for bunker busting missiles/bombs?
I'd say, from what I hear of the second movie, the aliens were the underdogs. Because they aren't smart enough to truly come up with truly war winning technologies. They could only make over-stupid elaborate machines of terror, not war
. Nor even use that engineering skill to make some seriously effective ecological advancements to not have to invade other cultures in the first place.