Content is sometimes removed, yes, but it's basically negligible.
Chitalian, the thing you posted doesn't read on my Chrome or Firefox -- do I have to be using a specific skin to get it to work? I would prefer not having content on every single page of the wiki that requires a certain skin to work. The Game Portals article was giving the same error for me, if that helps any.
Webber, we already list the games within the article itself -- virtually every article has an infobox listing appearances, and then anything introduced or removed in rereleases gets notated (or should). Even if we're not using them as a timeline, the icons are very much meant to be "at-a-glance" -- if the main way an article is communicating its topic's appearances is through the icons, then it's doing it wrong.
If we reduce things to having one icon per "story", we should have a max of nine icons per page (ten if we treat BbS 0.2 as a separate "story" rather than a new episode, and poss. a few more if we include the manga/other media icons) Most articles will have far less than those nine.
Building on the above -- I'm wary of making the game icons much more code-complex than they already are. For one, unless we can figure out a way to template Nezzy's example without having to change the on-the-page code much from what it is now, it's likely to be impossible to add to new pages correctly without a primer, meaning we'd have to wait on long-term wikiprojects to get pages edited. For two, it makes the articles a nightmare on slow computers or mobile users.