If that is easier for you go for it, it is easier for me with user.config and easier to support. I don't want to fool with diff tools when maintaining production sites, I only have a few customizations and I would rather restore them by hand and know they are done correctly.
Also Web.config is under source control so those of us working from the repository prefer using user.config and do as little modification as possible to Web.config
Also providing support for mojoPortal on a daily basis, I think user.config is a much easier thing to explain, I can't go telling people they need to use diff tools to upgrade their site, it will be difficult to support.
Best,
Joe