To be sure, this is an incomplete list, but it is a good start. Here's what I don't like about LINQ to SQL:

• It only works with MSSQL. Yes, this point has been beaten to death, but it is entirely justified. Third party solutions don't cut it. LINQ to SQL intentionally seeks to exclude a sizeable population because of this hair-brained decision.
• No way to easily specify adhoc LINQ queries. This doesn't count. I know the benefits of design-time queries, but I should also be allowed to shoot myself to get the added flexibility if I so choose. Building up expression trees is not a viable option for every day development.
• The constant labeling of LINQ to SQL as an OR/M. That label considerably overstates what this technology does. One to one mapping between a table and a class is not really OR/M. It seems like they want to force you to change your database by writing stored procs and views to make your object model better.
• There is no automated way to easily pick up changes to the database schema.
• There is no easy way to preserve changes to the generated code. e.g. I change the name of the automatically generated class from collection_details to CollectionDetails, but I evolve the schema of the table. When I re-add the table, I need to set all of the custom properties again. I know I shouldn't change generated code, but see the next point.
• Speaking of collection_details, it would be much better if the underlying class generator had some options to clean up legacy table names (e.g. remove underscores, camel case resulting table and column names).
• No many-to-many support. In short, when you have an junction table (aka associative table or cross-reference table), you will need to write code like this: User.UserPermissions[0].Permission vs. User.Permissions[0]. Until we see LINQ to Entity (if ever), we do have this, but you can't use the new entity in a LINQ query.
• There is no built-in solution to using LINQ across tiers. I don't want to expose my LINQ classes (see the point above about the tight coupling between database and objects) as I may want to change my database, and I don't want that cascading to all of the places that use it. There is also no diffgram, so even if I did it, I would have to write my own change tracking and resolving support. I went to an OpenSpaces meeting on this very topic during CodeMash, and the consensus was not flattering.

In short, it seems like this part of LINQ was released way before it was ready. But it does demo well...

Feel free to add your own grievance to the comments.