I'm not sure where I sit on this... it's almost a toss-up, although ToD is probably in the lead. I saw KotCS twice on opening day; the first time through I didn't know what to think.
What I came out of it with (especially the second time) was that yeah, the CGI is a little weird at times, but I think it's just another one of those quirks that'll blend with the oddities of the other films, once the newness has worn off. The crystal skull thing was cool, but I think it could have been developed better. It seemed a little easy, comparatively. (But maybe that's because Mutt was a big help?) I think the jungle and the beginning were some of the best fight sequences in the series, though. Tied with (if not exceeding) LC's tank fight.
It's got a lot of things going for it, but perhaps not enough.