I'd have to go with A. The aliens don't have any other aliens outside their own group of species to test it on, so naturally weapons technology is going to develop towards the most efficient way of slaying members of that particular group of aliens, as its all weapon designers have to go on. Even if the weapons were meant only for use on emerging species, the weapons designers can't predict that. That said, if the biology and technology of both the current group of aliens and the discovered species is similar, naturally this doesn't apply, but even if the aliens technology is superior to the emerging species, chances are the aliens own weapons are going to be more effective proportionate to their power than the emerging species weapons, and the same applies with the emerging species weapons.
A good example is the covenant. Plasma rifles are perfect for cutting through heavy shields, but you're going to take a beating if you deploy them against heavily armoured space marines who don't have shields and instead rely on heavy armour and bullet hoses. In this case it was only the fact that elites shields are also resistant to impact damage, and being physically much stronger than the marines, which allowed them to hold their edge. This changes if the two groups have been at war with each other for a while. For example, the brutes developed impact weapons, and had this been reality, this would probably have stemmed from the fact that the humans the weapons were designed to kill wear heavy armour instead of shields so impact weapons are simply more effective. Master chief doesn't count, as he's only one man and however dangerous, the brutes are not going to design their entire armoury around killing him (Though that might be wise...) Similarly, you're going to be able to shred human armour with concentrated fire much more quickly than you can burn through it. (Though this obviously doesn't apply to skin.) So human weapons tended to be weighted in this direction. Both sides were masters of their arts, problem being that there were two different development paths meeting. And of course, the humans simply didn't have the technology to build energy weapons (with the exception of the spartan laser, which considering its unwieldy nature was probably a prototype.) But even if they could, and had the war with the covenant not broken out, energy weapons wouldn't have come into their own until shields were commonplace, in my opinion anyway.