WMT "Links to Your Site" not featuring good anchor text

[onlinesource]

Let's say I have two domains, www.tshirtshop.tld and tshirtstore.tld. The shop site has been ranking well and the store site is struggling. So today I checked Google Webmaster Tools and compare the "Links to My Site" on both sites. This is what I discovered.

The anchor links under "How your data is linked" according to Google for the shop site are.

1. tshirts
2. shipping details
3. buy tshirts
4. buy cotton tshirts

OK, pretty good. So then I check the store site and it comes up as.

1. shipping
2. faq guide
3. contact us

So both sites have headers and footers and both sites have the same generic type of links on both, but why would Google be ignoring the generic links on one site and concentrating on keyword-rich anchor links on that site but not the other? Is this a big deal at all?

[nakkers]

Are you referring to internal links when you say "both sites have headers and footers"?

[onlinesource]

Yes, this problem relates to internal links. Internal links are what seems to be appearing as "How your data is linked" in Google Webmaster Tools. GWT seems to be pulling anchor text from internal links on my site such as "contact us", "privacy policy" etc instead of focusing on more keyword rich anchor text such as "tshirts" or "buy tshirts" like the shop site does. I don't understand why Google can navigate towards the anchor text I want it to on the shop site but not the store site.

The one possible factor that I did not mention before, was that the store site's shopping cart is setup with multiple store views that include international domains like tshortshop.eu or tshirtshop.ca. I did this to help drive traffic in international search engines like Google Canada. On the surface all of these sites visually LOOK the same. It's like how Cafe Press has multiple international stores that share the same database, but the difference is products viewed by certain countries show their currencies and weight preferences. Otherwise, they are pretty darn close. My question is, is it possible that Google sees all of these international stores as being the same and since it's seeing what it could be believed to be duplicate content, it's ignoring specific anchor text that I want it to see? I do use hreflang tags in the code to set store views for each area though. Maybe the hreflang tags are not working? Would it be wise to setup these stores as subfolders instead, and make them an extension of the store, like tshortstore.tld/ca for Canada, or is that not really the issue here?

I do find it strange that Google can not focus on what I want it to focus on like "tshirts" and "buy tshirts"... which to me is either a problem with the site's structure, because it seems Google recognizes generic text or anchor text in the headers and footers and sidebars as a WHOLE rather than focus on the unique content within the body. I know a lot of sites have generic footer links, but Google doesn't focus 100% of their attention on them. Or the issue is because of something else?

[lucy24]

it seems Google recognizes generic text or anchor text in the headers and footers and sidebars as a WHOLE

This is one of the many areas where you look at what GWT tells you, shrug and move on. Yes, they do mix your internal links in with the "real" links. Just be glad it's not showing up as "Click here" ;)

Detour to my own GWT/GSC tells me that I've got an increasing number of links in the form "HTML with commentary" or similar, which is depressingly uninformative but an artifact of the way this particular directory is structured so there's not a darn thing I can do about it. Fortunately it doesn't prevent humans from clicking the right thing.

[onlinesource]

Ok, so there is no way to improve the results OR the results don't really matter? Either way, it's nothing worth harping over? :)