That does seem weird. It's never happened on any of the iOS devices at home (iPhone, iPad, and iPod touch). I do buy lots of apps, but so far walang problem naman with syncing apps. If ever, the only problem I ran into was album art getting messed up sa songs that I bought in the iTunes store. Haven't resolved that one though.
If I understand you right, the problem is that your apps don't show up sa iPad after syncing? If so, have you tried getting them on the iPad directly? You can access your purchased apps sa App Store app on the latest iOS. You can download them directly on any iOS device provided that you're signed in with your Apple ID and you haven't reached the 8(?) device limit. They have a record naman of all the purchased apps eh (including the ones you got for free).
Agree with 3G on iPad, di sulit for me. I can always use the mobile Wifi or magtether nalang sa iPhone pag kailangan talaga.
On space.. agree rin. 32GB din lang iPad ko, but I wish I had the 64GB. Lalo na since it's really an entertainment device for songs, movies, apps, and books. Didn't expect that. Music palang, half na taken. The apps are pretty big as well (I think ~10GB). Sa movies, watch then delete nalang ako.