I think the stitching problems on the welt/sole would bother me the most especially considering they are supposed to be first quality. Unless you bought them for maybe 50% off or better, I vote return.
Thanks everyone, I'm going to return for another pair. Worse that can happen is they send me another bad pair, in which case I'll just pass. To those who favored keeping, I understand your points, but I think all the problems taken as a whole just make for an unsatisfactory shoe (even had they been seconds).
As an additional note to anyone considering purchasing the Brooks Brothers version of the Dundee (there is also a brown grain version), these are considerably tighter fitting. My AE Dundee's allow me to wear all but the thickest socks I own. Due to the Brooks Bros. insole, it seems I can only wear these with thin socks.