What you seem to be forgeting is that most NPCs already have crappy stats by default.
Think from the viewpoint of the inhabitants of D&D world.
Only a few peopleb out of the total population have the actual stats to make decent wizards/sorcerors.
Plus a sorceror/wizard needs years of training before they even get the first level of their spells (also known as character starting age).
Regular Eberron Dragonmarks however mean that House whatever can harness high-level spells from average people whitout needing to sink years in their training.
If anything, I always saw dragonmarks as a way you could get a bunch of level-apropriate magic whitout actually being a fullcaster.
To get the Lesser and Greater marks though, a character will have to be 6th and 9th level respectively. This means that in order to cater to most of the population, a significant portion of NPC's in the Houses will be 6h and 9th level (especially considering they can only use their Dragonmark powers once or twice a day). This seems a bit weird (I don't really recall seeing any statted NPC's with NPC classes in the books that are that high in level). And if the NPC's with NPC classes in the Houses are that high level than why aren't the NPC classes out of the Houses that high level? Do the ones in the Houses just work harder?
It's not a bad option at all but I think it invalidates my idea either.
Anyway, claiming "Low level NPCs can now get high level SLAs and you can't nyah nyah!" sounds like an horrible plan to me.
I definitely wouldn't recommend springing this on an unsuspecting group. Present it to them and ask if they're okay with it. This is an idea that is intended to primarily have flavor-based impact on the setting after all.
I suppose you could allow the PC's to get the feats but the group would have to be okay with the non-dragonmarked characters being less powerful than the dragonmarked ones. The ones with the dragonmarks would also have to be okay with being under the control of their House.
Dragonmarks aren't just useful for their direct effects. There's a lot of items in Eberron which can only be used properly by someone with a dragonmark (e.g. a cheap teleportation circle powered by charges from a Mark of Travel, or the reins used to control elemental vessels). Then there's those PrCs with dragonmarks as prereqs, though they probably don't have much impact on the larger scale.
Kieth Baker gave this as the explanation for the Houses prominence as well. Frankly, I personally don't like it. What's the point of even giving the dragonamrks these weak primary effects when the real power comes from the magic items that use them? It feels forced and artificial to me. Having someone use the innate power of the Mark of Travel to Teleport you somewhere just seems cooler to me than using it to power a magic item that will then take you somewhere.