let's compare those covers:
We can see both groundon and kyogre look a bit different.
Groundon:
It now has a glowing yellowish part where were those black lines, almost like it was in lava, it also changed a bit it's pattern.
Take a look at it right paw, it now is a bit different and has the omega symbol,
Those 4 sharp claws in his tail are now flexible, almost like fingers on a hand.
it also has many differences minor differences, like on it's belly it has some sharpy yellowish things that come from those lines on it's top.
Kyogre:
The red lines it had on it's body, have changed to two tones of light blue and very light yellow, similar to groundon's lines.
I has also changed the pattern, we can clearly see a circle and some other marks on it's head and a line that cross hif body.
We can also see those flippers on it's top-back part aren't there anymore.
It's tail look now soft and flexiblem and changing with the stream.
It has an alpha symbol on it's paws.
Ruby and Saphire had no mention about greek letters and those legendaries look different.
Pokemon states this as "an epic new adventure", although I think we'll be seeing Hoenn, I think it won't be just a remake,
this is probably a sequel or a half remake, where part of it would be like R/S/E and part would be new,
this whole alpha and omega thing makes me think there is more in it than just a remake.