When trying to retreive items from a list which uses a Site Column that is a looukp column to a list in a different web, we get the error:

{error":{"code":"-1, Microsoft.SharePoint.SPException","message":{"lang":"en-US","value":"The field 'TrouserSize' is not supported in query. The lookup list is in another web."}}}

As provisioning process, we would love to either add apps from app catalog or store directly using CSOM APIs. This should include the 'I Trust it' model as well. This will help in automating the entire site/sub-site provisioning and making sure apps are available after site is created.

At the moment it does not seem possible to create WebPart connections via the Client Side Object Model.

Currently term store operations are only available via JSOM. It would be nice to see this added to the REST API as well.

One should be able to download an older version of a file using something like:
FileInformation info = File.OpenBinaryDirect(context, "/" + _fileVersion.Url);

But instead that throws a 401 error.

See MSDN thread here: http://social.msdn.microsoft.com/Forums/en-US/7746d857-d351-49cc-b2f0-496663239e02/how-to-download-a-file-version-from-office-365-using-csom?forum=sharepointdevelopment

The latest version of the SharePoint Framework Yeoman generator contains a mix of features that are GA and preview features (for example connecting to MS Graph, web part connections, extensions). Whether the generated solution can be run in production depends on the features used to build the web part. With that, when bundling the project, the toolchain should warn of any experimental features being used in the project which would prevent the solution from being deployed to production tenants. This would help developers avoid deploying solutions depending on experimental features to production tenants, only to see the deployment fail.

Provide the Version History feature on list items with CSOM, i.e. provide which metadata has changed with the previous value.
Currently, the only way to retrieve versions is through the FileVersionCollection/FileVersion objects which provides only the VersionLabel, CreatedBy, CreationDate and Version Url.

Ideally, we would need a ListItem object holding all the attributes and values for each version - or at least the attributes that have changed.

Some list/library settings are available via CSOM. Others are available via the list property bag (although that approach is not desirable). However, there are even other advanced settings that don't appear to be accessible (read or write) via CSOM/REST. In particular, the advanced settings for "open documents in the browser" (open in the client application, etc.) or allow "quick edit" (yes/now).

I'm looking at SharePoint 2013 when trying to do this, but I suspect the same problem occurs for SharePoint Online and SharePoint 2016.

The only way to expand SharePoint events from a calendar is using CAML. There should be a way to retrieve the recurring events fully expanded using REST.

There's currently no better way to configure search indexed and managed properties than export/import configuration. It's a huge pain when building search related apps and a black box, we need something better

Actually, the only way to paginate list items using the new REST APIs is to use __next property. There's no way to have a full working pagination using $top and $skip token as for any other REST call.
See my comment here:
http://msdn.microsoft.com/library/d4b5c277-ed50-420c-8a9b-860342284b72.aspx

Provide option to enable\disable event firing from Remote Event Receivers in SharePoint Online (CSOM/API) similar to SSOM - EventFiringEnabled

You cannot currently use CSOM to publish content types in a content type hub in O365. Right now you must imitate the page post back to do it.

App-only policy in the SharePoint App Model is very restricted regarding Taxonomy operations. Even if an app is granted full control over the tenant, it lacks the permission to do anything but read operations on Taxonomy. Please provide the ability to create Groups, Term Sets and terms using app-only policy.

Currently term store operations are only available via JSOM. It would be nice to see this added to the REST API as well.

Support .NET Core with CSOM

Currently it's not possible to set the List.NavigateForFormsPages property through CSOM as it is in the server API.