So the Evangelist gets two domains at level 1, +1 at 5/10/15/20. That ends up at six domains, which is a lot!

Here's the catch, though: with some notable exceptions (Elder Evil's Sertrous (comes with free [Vile] feats!), Eberron's Sovereign Host, and clerics worshiping an ideal), most gods don't have six domains. I think it's usually closer to fiveish, maybe?
Except for Core gods, because they're the only ones that are actually assumed to be part of the setting and thus get bunches of new domains whenever a new list comes out. Pelor goes from having four domains in Core to nine with splatbooks and twelve with Dragon Magazine.

I'm not sure why they went for +1/5 levels, really, when the standard PHB number of domains is 4?
Especially when you've got stuff like Deities and Demigods suggesting that
A deity has at least three domains. Deities can have more than three domains if they possess the Extra Domain salient divine ability.
This isn't really a problem with the variant's power as much as I just find it a puzzling design decision, though.


Also, well, unless you're worshiping one of the big three (Sertrous, Sovereign Host, an ideal) then you're kind of going to be pigeonholed eventually by what god you choose. If you choose Vecna because you like the look of Knowledge and Magic, well, I hope you like the Evil domain.
Not that this stops you from being really powerful, it's just that if you're not careful it's easy to end up with a "wasted" class feature. (That comes at, like, level 20. So you'll multiclass or prestige out before then, probably.)
It's a weird design issue, really, since the sixth domain you grab is almost by definition going to be the least attractive one. It's not really that much of a capstone.