Latency appear to be an issue with linked server
The queries are simple selects from single tables.


There are a number of details that you need to include that may have an effect here. Are they many small resultsets (a few rows or small rows) or small numbers of large results (many rows and/or large columns like BLOBs)? If it is a mix can you separate them out and test the performance separately?

How are you making SELECTS to the remote end? Direct inserts into a local table with something like INSERT localtable SELECT stuff FROM server.db.schema.table or are you reading the results into your own code for further processing before INSERT? If the latter than you might need to look into which cursor options you (or the framework you are calling through) are using and see if there are less latency sensitive options that are applicable (assuming the framework you are using allows you this level of control). If the options used mean that each row is request separately then latency will be far more of an issue then if they allow the rows to be read over the network in bulk and navigated locally.


  Setting this up in SSIS improves performance to an acceptable level


If you are using exactly the same statements to retrieve the data in SSIS as your previous method then that could imply one of three things, or a mix of them:


The cursor options as mentioned above (SSIS is more likely to be favour latency friendly options which may in other circumstances be sub-optimal, because it is more often used to work with more widely distributed servers)
Connection pooling which your current method might not be making as much advantage of (again, here we need more details to do more than guess). SSIS will use the same connection rather than renegotiating for each query, your other process may not be doing this.
Possibly concurrency: is your workflow in SSIS allowing it to submit several queries at the same time, so it can submit new queries to the remote end without first having to wait for the previous ones to complete, where the workflow in your current process is entirely sequential?