Will all games be Bundled?

Not while Activision lives.

Yes, at least a large portion of the games that are released will get bundled at some point (not all, mind you), but you still have the window between its release and it getting bundled to get full CV from it. For games that do well, it will (probably) take a while before it gets bundled, but games that don't sell well at all are more likely to get bundled soon after release.

I can already see it getting a problem. For my recent alphabet train I had an awful time trying to find unbundled games for some letters (without spending enough to need a mortgage on my Steam wallet), there are just so many titles now that have been bundled.

Given the sheer amount of garbage being released on Steam these days, I don't think most games will ever be bundled. Unless of course you get 100 for $1 which would definitely be a fair price.

These stats are a little old, but I have a tally of all games released on Steam vs. newly bundled games from October 2013 to February 2014. I only posted October and November though.
http://www.steamgifts.com/discussion/GdaTt/october-steam-releases-vs-bundle-list-additions
http://www.steamgifts.com/discussion/VxS0Y/november-steam-releases-vs-bundle-list-additions

Rate of games being added to the Steam store has at least doubled since back then, and I believe that the rate of newly bundled games has been decreasing, since at this point most bundles have at least a couple of rebundles.