I've had this issue twice in the past. Once was because of a conflict between All In One SEO and another plugin which was fixed by updating the plugins. The second time was after a theme change where it turned out the theme had an internal suite of SEO tools that were adding the secondary description which was fixed by shutting off those features. Without knowing all the details of your wordpress site, its a bit hard to determine the exact cause. Check that your theme doesn't have a function interfering with All In One and try turning off plugins to see if any of them are in conflict. Could be as simple as needing an update.

The canonical should pass link equity similar to a 301 redirect.

I agree with Everett from a standpoint of User Experience. It could potentially be better for users if they appeared on a product page where they could then choose color, size, etc. variables for their product instead of having to click through multiple pages to find the right one or scroll through a huge list of variations.

The reduction in pages should also help consolidate link equity and keep pages from cannibalizing each other in the SERPs.

As for Takeshi's suggestion on Canonicals, I'm a fan of the rel=canonical tag but the potential problem with using them in this instance is twofold. 1) As Takeshi mentioned: "as far as Google is concerned you only have 1 page with the content on it" and 2) Canonicals are suggestions not directives so the search engines may choose not to recognize it if not used properly.

Similar to what BJS1976 and Takeshi stated, the way we handled the bulk of duplicate content issues from a similar circumstance for our ecommerce site was handling the different varieties of the same product through parameters and then canonicalizing the parameters to the version of the URL sans parameter.

For example, due to database reasons /product1.php?color=42 and /product1.php?color=30 are the same product but one is red and one is blue, the pages are exactly the same & have radials/buttons/dropdowns to choose any available color, /product1.php would default to one specific variation we chose (usually the best selling color) and then /product1.php?color=42 and /product1.php?color=30 had a rel=canonical tag added pointing at /product1.php

For any remaining products flagged as duplicates that couldn't be fixed that way, we set those aside to have myself and another copywriter work on creating further content that would set them apart enough as to not be duplicates.

It is always best to do a one to one redirect instead of a chain. As Federico said, there is some pagerank loss when doing a redirect (though the exact amount is debatable and may be neglible) and redirecting A to B to C compounds the problem. On top of that, too many redirects in a chain will lead Googlebot to stop crawling the chain. One or two is fine, three or more is not. In this older video http://youtu.be/r1lVPrYoBkA Matt Cutts started talking about redirect chains at around 2:48 and mentions that one, two and maybe three in a chain is fine. This Whiteboard Interview from 2010 with Matt Cutts http://moz.com/blog/whiteboard-interview-googles-matt-cutts-on-redirects-trust-more also states the 1 or 2 301s in a chain. So if you're redirecting  A -> B -> C -> D -> E -> F... you're possibly hurting yourself. Where possible you should change the redirects so its A to F, B to F, C to F, D to F and E to F. As for removing the redirects after a certain number of months, I'd check to see how many people are still linking in with that older URL. You'd want to ask sites linking in to update to the newest URL before you 404 it and lose those links. And if you're still getting tons of direct traffic coming in on an old 301 then you might want to do some digging & research before you cut off that traffic. Odds are though after a few months you wouldn't be getting as much traffic coming through on the older URL but there is always the possibility.

Because Google has never broken its own guidelines and then penalized its own pages before.... http://searchengineland.com/google-penalizes-google-japan-16541
http://searchengineland.com/google-chrome-page-will-have-pagerank-reduced-due-to-sponsored-posts-106551

There are no issues with connecting multiple sites to one email account in analytics and WMT. Would get pretty hard to handle if everyone needed a brand new email address for every single site they tracked.