If you could narrow down which file types are giving you the dramatic problems and look at their size?
I would have reccomended using PDF / PSD images as I don't care what anyone says - there is an incredible difference between those two file types and JPG/TIFF format on the iPad 3 for sure!
But with great clarity there comes a lot of fussing around the file size...
it also depends what type of states your images are within - e.g. if your page is just a static image then the builder panel takes a kind of screen shot, so you can get away with scaling your images down within photoshop or whatever.
but if you're having the images in any kind of overlay - the image is held, not captured which makes it very data heavy...
hopefully that all makes sense, i'm not the best at articulating my point!!
My advice is, go through (I know it's a pain) and just check which images are causing the problem and work down from there, scale some - change the formats of others - experiment; because these tools are the most inconsistant things I have ever worked with, and who knows! you'll probably get the most surprising results!!
I suggest taking a look at Colin's document on best practices for targeting the iPad 3: http://wwwimages.adobe.com/www.adobe.com/content/dam/Adobe/en/devnet/digitalpublishingsuit e/pdfs/dps-ipad3-bestpractice-apr2012.pdf. He talks about which overlays will automatically resample images to the right size, and which will pass the image through directly untouched.