I think the biggest thing, for me, is changing the way Dragonmarks work. I don't think they've worked great in any edition, to be honest; even in 3.5 they over-emphasized the SLA's when the main point was, at least according to KB, the skill buffs that allowed the Dragonmarked Houses to establish their economic monopolies (and the ability to use Siberys shard magic items, which further allowed them to monopolize certain industries). I have a sneaking suspicion that the SLA's were added to make them worth the feat.
Since I wouldn't want to use feats to express Dragonmarks I'd instead use the Blessings system and indeed focus more on the skill boosts and ability to attune to/use Siberys shard items. I might add a cantrip and then some ritual casting as the mark grows. I'd leave the actual spell-casting to Aberrant marks, to further emphasize how different those are from true marks.
Other than that? I'd tone the "magical war economy" aspects somewhat; rather than concrete mathematical bonuses the mass-produced magical weapons/armor would come with other benefits that would extremely useful for an army at war without providing straight to-hit/damage buffs (like self-repairing armor, blades that never dull, etc.) Any kind of magic artillery (such as eternal wands, or as 5e calls them, wands) would have been rare and powerful; probably what kept Aundair and Cyre in the war in spite of their circumstances. The 5e Treaty of Galifar would likely have included a fairly strict "wand control" policy that would have seen most such items destroyed in light of the Mourning.
There's undoubtedly going to be clamoring for an Artificer class and magic item creation rules, but I'd personally axe that class and have most magic item creation monopolized by House Cannith; schemas for even the most basic magic items are closely guarded house secrets, and again anything that would be regarded as a magical weapon of any kind would be strictly forbidden by the treaty. That's probably not a popular idea so that's more my personal Eberron than anything I'd actually like to see in official support. I mean... I'd be pleasantly surprised if that were the case, but I'd also understand the outcries of heresy that would spark.