Both cases make absolute sense to me. Ho-oh was all about testing the connection between trainer and Pokémon, hence Heart. Lugia was basically this massive sea beast that you had to tame and became a great ally, hence you needed great determination or soul.
Alpha and Omega refers to, of course, the beginning that Kyogre and Groudon are - creating the land and sea - and the fact that their Primals are so ridiculously powerful that they could bring about the end of the world as we know it.
I more meant the game actually explaining it instead of letting us come up with the answer. I could come up with possible connections with the additional words, here's another take on things:
Heart Gold: In Johto's mythology, Ho-Oh perched on the Tin/Bell Tower which is said where Pokemon went to be "awakened", which could be interpreted as meaning being born or are given life. The "heart" is often portrayed in many cultures as being the symbol of life. Thus we can connect Heart and Ho-Oh (who itself is based on various Phoenix mythology who have long/immortal lives and can resurrect themselves or others) together with both representing "life".
Soul Silver: In Johto's mythology, Lugia perched on the Brass/Burned Tower which is said where Pokemon went to "rest", which could be interpreted as meaning to die. The soul is often thought as what a person truly is, thus when you die your soul leaves your earthly body behind as it goes on to the after life. Thus we can connect Soul and Lugia (who has connections with oceans and storms, a deadly combination) together with both representing "death".
Yes, Ho-Oh and Lugia were the original Life and Death Pokemon, Xerneas and Yveltal are just more blatant about it.
Omega Ruby: Omega means "end" which, from what we heard of ORAS's story, could mean a few things. It could mean Team Magma's overall goal to "end" the age or humans and Pokemon trying to coexist so that humans can finally become the definite dominant species on the planet thus needing more land to expand. It could also mean all end to life as we'll know it since most if not all life on Earth needs water to live and Primal Groudon will try to evaporate ALL water leaving Earth as a barren wasteland.
Alpha Sapphire: Alpha means "beginning" and unlike Omega it sort of all points to once concept: all life began in the water. Team Aqua's plan is to expand the oceans since that's where life came from, and Primal Kougra will pretty much cover the entire planet in water allowing aquatic life to prosper and thus bring in a new age and opportunity for new kind of lifeforms.
... SO there's also sort of a life-death theme going on here... beginning to think Xerneas and Yveltal weren't really needed...
