The rumour that Elsevier is buying Mendeley has been greeted with a mixture of horror, anger, peppered with a few congratulations, I told you so's, and touting for new customers:
Here's some probably worthless speculation to add to the mix. Disclosure: I use Mendeley to manage 100,000's of references, and use the API for various projects. I'm not paying customer (but I do pay for some Internet services such as DropBox, BackBlaze, and Spotify, so it's not that I won't pay, it's just that the service Mendeley charge for doesn't interest me). I've published in Elsevier journals (most recently a couple of papers that, thanks to the efforts of Paul Craze, editor of TREE, are "free" in the sense you can download the PDF for free), and I took part in the Elsevier Grand Challenge.
So, given that I'm suitably compromised, here are some thoughts.
Elsevier are big, ugly, and at the corporate level are doing things that actively make researchers angry (see The Cost of Knowledge).
Elsevier are one of the most innovative science publishers around. They fund challenges, are investing heavily in interactive and semantic markup of papers (for example, interactive phylogenies), and have built an app ecosystem on their publishing platform.
Mendeley is suffering some from serious failings, most of which could be addressed with sufficient resources. The API sucks, mostly because Mendeley themselves don't actually use it. The Desktop client communicates with Mendeley's database using a different protocol, hence the API lacks the functionality needed to make truly great apps on the platform. The algorithms Mendeley use to de-duplicate their catalogue are flawed, occasionally creating entirely fictional entries.
The way Mendeley engineered the creation of a bibliographic database in the cloud is genius, as is their recognition that the object around which scientists will cluster is the article, not the author. They helped foster the altmetrics movement, and have a great presence on Twitter and at conferences (i.e., you can talk to actual people who write code).
What happens next?
Let's assume that Elsevier does, indeed, buy Mendeley, and wants to do interesting things with Mendeley, and that Mendeley doesn't become one of the many startups that have a successful "exit" for the founders but ends up dying in the bosom of a larger company. Here are some possibilities.
Mendeley becomes iTunes for papers
Forget the "Last.fm" of papers, what about the "iTunes of papers"?. Big publishers are facing a revolt over the cost of institutional subscriptions, and journals are increasingly irrelevant as aggregations. The literature that people read is widely scattered across different outlets. Journals are archaic in the same way that music albums are mostly a thing of the past, people mix and match singles.
In the recent fight between UC Davis and Nature, Nature estimated that "CDL will be paying roughly $0.56 per download". So, why not charge a buck a paper? Mendeley's web interface is practically crying out for a "BUY THIS PAPER" button. Under this model, Elsevier has an outlet for its content that doesn't force people to subscribe to large amounts of stuff they don't want. Mendeley could be used to establish a relationship directly with paying customers, rather than institutions.
Mendeley becomes the de facto measure of research impact
But combining Mendeley's readership data with citations, Elsevier could construct powerful measures of research impact, bringing altmetrics into the mainstream. Couple this with links to institutions, and Elsevier could provide universities with all the data they need to evaluate academic performance (gulp).
Mendeley becomes an authoring tool
Managing references and inserting citations into manuscripts is one of the basic tasks facing an academic author. Authoring tools are evolving in the direction of being online, and embedding more semantic markup (e.g., these are taxon names, this is a chemical compound, this is a statement of causality). In a sense reference lists are the one form of structured markup we are already familiar with. Why not build on that and create an authoring platform?
Mendeley becomes the focus of post-publication review
Publishers have failed to crack the problem of post-publication review. Several provide the ability for readers to comment on an article online, but this has failed to take off. I think this is because the sociology is wrong, if you want a conversation you need to go where the people are, not expect them to come to you. Given that people are bookmaking papers in Mendeley, the next step is to get them to comment, or aggregate their annotations (in the same way that Amazon's Kindle can show you passages that others have highlighted).