NOTE I have not yet seen or investigated the new SharePoint 2010 capabilities. This post is totally based on very scant reports I have seen from the WPC09 and the reality may be completely different. Do your own investigation!
It appears that SharePoint 2010 has the ability to not only read data from 3rd party applications but also send data to those applications.
Now the current version of SharePoint (Enterprise Edition) has the ability to perform an action when a link is clicked. This usually involves opening up the native application’s form so that the users can perform some action. This is fine because all the business logic for that application is maintained and all that the BDC connection is doing is giving you a short cut to where you would have ended up in the application anyway.
Now if (big if) this new capability allows SharePoint Developers to write a BDC such that it sends data directly to the application either through a web service or (god forbid) the tables directly then there is the potential for a whole layer of business logic to be bypassed.
This gets even more serious when you consider that the implementers of a SharePoint solution are rarely the deployers of the ERP/LoB solution and are likely not to realise the implications of their actions.
It sounds like a fine idea if you have total internal control of your systems but when it meets the real world it sounds like the scenario only a lawyer would love