Can't really speak to the artificer and seeker as I don't have much experience with them.
The runepriest is a pretty solid class right now imho. The problems with it though are that a) the rune feats are by and large a trap (i.e. you take all of them or none of them) and b) its incredibly fiddly which sucks for a lot of players.
For Rune Feats, I would propose modifying them to read you get a bonus of 2 + the number of rune feats (or other rune feats, etc.) up to a max of X. I don't know what X would be, but at least it would make a rune feat useful out of the gate. As it stands now though, the rune feats are not really all that useful until you've collected at least 3 of them. I suppose a human runepriest could have 3 by 2nd level, but then they haven't take Expertise yet. For non-humans it gets even worse. A feat, imo, should be useful the moment you take it, rather than having to wait for a couple of levels (and a couple more feats) for it to become useful. Add a few more rune feats to the mix along with the above change, and now you get a nice, flavorful option.
As for the fiddlyness, I'm not sure. Leaders in general have a tendency to get fiddly from time to time but the runepriest seems to be a particularly potent offender. Part of this is, I'm sure, due to the relative lack of healing (and thus the candy the runepriest hands out becomes the balancer) but it still makes it fairly complicated to play. Personally, I'm not too put off by it, by I know others are. More to the point, if I miss a session, nobody else can really run the character in my absence as you really do need to play the character to understand how it works.
The only final thing I might add is a build that uses Int as a secondary stat. This is mainly because its a bit annoying that runepriests get auto-training in religion but have otherwise very little need to boost Int. At the very least it would be the third option, and likely the fourth for most players. Its a minor thing, but annoying all the same.