Multiple approaches here.
First, you can open the PlayStore App, hit the menu button, go to settings, and advise it to only work with WLAN, plus not install apps automatically. This would cover part of your problem.
Second, you could also tell it to not check for updates at all. While on a first look this seems to contradict with your intention -- please read on. Go and install yourself the Appbrain App Market App. This actually utilizes the Google Play store, it is not a separate market. It even uses your Google account for everything. Now synchronize your installed apps with the AppBrain App. After that, you will see available updates -- and you can decide on a per-app basis whether to...
- accept this update
- skip this update only (and be reminded only for the next update)
- skip updates for this app altogether
As you told the "original" PlayStore-App to "shut up", there won't be multiple update notifications. Just use the Appbrain App for updating your apps -- it will do so by calling the PlayStore app using its API. Batch-Updates ("Update all") are of course possible as well.