Really despise those "surprise" ads...
I completely understand the need for ads (revenue), but not this format. I would like to suggest banner ads instead, at the top or bottom of the screen. This "surprise ad" format has always felt like an underhanded and cheap way to get ad views; right as you go to tap something, an ad appears, thus making you tap IT instead. Highly despised.
However, if you want to keep the full-screen ads, I play a casual town-building game that handles these rather gracefully, by all rights:
The full-screen ads appear every 15-20 minutes, however... Before they appear, a small countdown banner appears on the left side of the screen, giving a full ten seconds to finish an action before then showing the ad. I've yet to see any other game (or app, for that matter) use that system; as someone who hates those "surprise" ads, it's a considerate warning that I greatly appreciate.
I'm quite fond of Vault by this point, and would much rather not uninstall over these. I look forward to seeing your solution. :)
(NOTE: If you want to see this system in action, the game in question is Townsmen, by HandyGames. No, I'm not trying to trick you into playing! :D )