so if I do a cloud setup on my new iPad I still can connect it to my computer for app installs?
I would prefer to be able to do both local backup and cloud backup but when I tried it (alternating backups between computer and cloud) on my old iPhone 3GS it only lead to problems
A cloud backup wouldn't be able to install the apps that have been removed from the store/purchase lists since they "don't exist". You could install those manually from your local iTunes afterwards but they would be without save games or personal settings intact.
A local backup would be able to retain settings and such even for those apps if local copies of those apps were kept.
Personally I have both cloud and local iTunes backups since many apps that I have bought have ceased to exist (iMAME or iDOS for example). Not sure what problems you speak of, when time comes to restore its simply a matter of picking from where to restore from.