Remote deployment to WebSphere servers is broken in MyEclipse Blue 9.1. This issue has been internally fixed and will be released as part of the 9.1.1 maintenance release due in a few weeks.
Until then, users on 9.1 who wish to apply the fix immediately can do so by following these steps:
1) Download the archived update site attached to this post. (you must be logged in to see the attachment)
2) In Blue, go to Help > MyEclipse Configuration Center and click the Software tab
3) In the Browse Software section on the left, click Add Site and type in any name for the site. Click "Add from Archive File" and select the file you downloaded in step #1.
4) In the Browse Software section, you will notice the site you added under "Personal Sites". Expand the site to find "MyEclipse Blue Edition", right click this and choose "Add to Profile".
5) In the "Pending Updates" section, you will now notice 1 pending change. Apply this change, follow the wizard and restart when prompted.
This will update the plugins affected by this fix and remote deployment should now work.
I will update this thread when the 9.1.1 release is available. Thank you for your patience and sorry for the inconvenience caused.