I can't find anything about the wheels on either bike, aside from what Kona says about them. The Rove has a full Formula set. The Jake has Formula hubs with Alex "Black Dragon" rims. The Black Dragons look semi-deep section (~25mm, maybe), which probably means they'll be heavy but tough. I wouldn't expect either set of wheels to be anything special.

I do think the Jake frame looks nicer. Steel zealots will say that any steel frame is better than any aluminum frame, but the Jake frame has some nice features. I would definitely expect the Rove frame to be cheaper to produce. The geometry is fairly different, so that comes down to preference.

The Rove brakes are almost certainly better. The tires are the same make, so that's a wash. The Rove has a slightly nicer saddle, I guess (Comp vs. Sport). The Rove does have a Rival rear derailleur, but most it seems to come down to a marketing decision to price the Rove higher.

I don't think it's coincidence that the Rove is priced the same as the Apex-equipped Salsa Vaya 2. The nearest equivalent I can find to the Jake is the Jamis Bosanova, which is at $1275. I think the Jake is just a really good deal.