It depends on the game. I think a lot of those farm building type games have accounts that you log into so your progress would be kept by the relevant company's own server.
Other games line Inifinty Blade II and Swordigo keep your progress through iCloud.
Plenty of other games don't do it at all - but if you're up for a bit of jiggery pokery then you can use iExplorer to copy the save game files across - which is no good for continuous syncing, but it will get your iPad caught up with whe your iPhone is.