After having not played for a few months, coming back and seeing no scores for killing the aliens at the end of each mission was a bit of a shock. To be honest, I thought it was a bug. If I hadn't popped onto the forums tonight, I would never have found out about all these changes to scores and would have been pretty content to keep playing.
I guess I'm obligated to throw my bit of fuel onto this fire, though. Ground missions should in general be worth more than intercepting the UFO's because of public opinion. The aliens will succumb to our atmosphere given time, but the majority of the populace probably doesn't know that. If the local military is slow or inefficient and some aliens escape to do a little havoc, a lot of panic could result, especially in population-dense areas. So public opinion turns against whoever is in charge of the country, forcing a change in power to a less friendly head of state or simply causing the money that would be given to you to instead be used on riot police. This idea isn't without it's own holes, but I didn't see anyone mention citizen unsatisfaction so here it is.