The second problem is a paper wallet doesn't mean full security. If you enter a private key onto a compromised computer your bitcoins can be stolen in a fraction of a second. A paper wallet only keeps coins secure so long as they only exist with the paper wallet.
In theory that is true but I don't think it is very likely. I imagine after storing a portion of my coins for several months or even years I visit blockinfo.com, open my online wallet (2 factor auth.) and Import the keys in a few seconds. What are the odds that exactly that instant an attacker breaches my system?
The odds could be good actually.
The nature of bitcoins make them unbelievably attractive to hackers that are immoral. Their increasing adoption and value will only increase attempts to steal them.
If your computer or phone has bitcoin targeting malware then it can wait for the second you enter the private key to transfer bitcoins, assuming an Internet connection is available. The malware can make the transfer in fractions of a second, faster than you can block it. Two factor authentication means nothing if your bitcoins are transferred before you even access them.
Computers don't have the physical limits of humans. Waiting days, months or years to steal coins means nothing.
To increase security: a) several paper wallets only holding a fraction of your total b) always 'spending' the whole balance by using the aforementioned method.
The way you describe it above you enter the private key with the majority balance before sending the unspent balance back to a paper wallet. If your system is compromised the majority balance can be stolen before reaching the new wallet.
To me that seems pretty safe.
Security is only as strong as the weakest link in the chain. If you have good habits in general for avoiding malware, then yes you probably have little worry. The problem is unless you're pretty much a security expert you can't be sure how likely you are to have obtained malware.
About Trezor:
a) doesn't ship yet
b) like it in general but it still needs more technical skills and understanding than piper
c) you still have to connect trezor to your online device and how would I know that some future malware can't crack/infect it?
d) can only handle one wallet as far as I know
e) if so - I think it's to expensive at the moment
a) I imagine it will eventually
b) it provides a fuller security solution and so warrants the time to learn it, which is not much
c) malware can't infect it because it doesn't use an operating system; it's function specific
d) it can handle any bitcoin balance, small or large, securely
e) I think that depends