What do you mean by weaker against other Pokemon? Are you thinking of Zygarde by any chance o_O? Sure Rayquaza has weak defenses but it hits hard and fast (especially compared to recent legendary mascots) but it's not weak. Rayquaza's bonus for being the third version mascot is it's 10 bst points higher than the rest it seems, while Giratina got a forme, Kyurem got sequels and two formes despite being so weak in the originals, and Zygarde...may get a very powerful Mega?
Either way I hope that they make Delta (Mega) Rayquaza faster (since Delta means change, and change is associated with speed) than already normal Rayquaza. If they give it Aerilate it'll be a threat, well bigger than it already is...maybe it wouldn't even need the extra speed as it'll have STAB Extreme Speed.
They could give Groudon Flash Fire, and Kyogre Storm Drain.