For yum, it would be nice if you could yum -y update and get the updates. The problem is that it had over 100 rpms that it could successfully update if it would do its best. Up2date does the same thing, so not really an up2date vs. yum issue. With a customized and manually edited script, I could get yum to do what I wanted by using the information related to what up2date was trying to install.
I keep suggesting you use the yum shell and you don't seem to have tried it.
Try this, please:
yum shell
update transaction solve
<some error occurs here>
exclude package-that-causes-error update transaction solve
<no errors>
run quit
ta da!
-sv