I looked at the new "Deploy to organization" feature in TWS Spire 12, but there are problems.
First, "Deploy to organization" does not detect which files have changed and it does not check those selection boxes.
I have attached a screenshot example of how a deployment looks in Eclipse with the Force.com IDE. The changed files are highlighted in yellow, the action is Overwrite and the selection box is checked. The UNchnaged files are highlighted in gray, the action is Overwrite and the selection box is NOT checked.
In TWS Spire 12, ALL files in the project have an action of overwrite, but none of them are selected. You have to figure out for yourself which files have changed and check the selection box for those files. For a large project like mine, this becomes a very difficult task.
In addition, all files that exist in the target Salesforce instance but not in the project, appear in the deployment list with an action of Delete. None of these files are selected, so obviously they won't be deleted. But in the Eclipse Force.com IDE, files that exist in the target Salesforce instance, but not in the projejct, to not appear in the deployment list.
If a file that did exist in the project was deleted from the project (not removed, but deleted), only then should is appear in the "Deploy to organization" with the Delete action.
The second problem has to do with the screen colors. I was using the blue color theme. This resulted in the "Deploy to organization" list having a white background with yellow text. This was impossible for me to read. I had to switch back to the dark color theme.