Instead of using the update manager, use synaptic to manage your software. I have disabled the update manager and only used synaptic (choose "never" in the ubpdate manager's option) It gives you a lot more control in terms of what you want to update, which packages you want to pin (no updates) etc. It also shows you a lot more infoemation and is a lot faster. It should be installed by default instead of the bloated Ubuntu Software Centre.
If your update wants to remove something, better find out what it does. If you use ppas then you should install ppa-purge, just in case..
sudo apt-get install synaptic
Finally, if you have 50 updates everytime you use Ubuntu it probably means you don't update or log into Ubuntu every often, I hardly have any most of the time except for things in a couple of ppas.
Also, I don't see a problems with a lot of updates, it does it in the background and doesn't nag you to reboot like Windows, just more freebies.