I had the same problem, particularly on the inside part of my foot, where the seam between the elastic and the rubber rubs really painfully against the bone. However, I just kept wearing them and a month or so later they're the most comfy shoe I've ever owned. Hmm.. honestly a lot of the best trad shoes are lace up, I guess you could check out the supermoccs?

I bought these super small to get a good fit for all kinds of climbing. I started out unable to walk in them but they are my go to comfy shoe now. They stretched continuously for almost 6 weeks. They are the perfect marriage between comfort and performance for me now. Keep wearing them, try wearing them around the house. They will break in. The upper will stretch out.