All of the examples that were cited doesn't really treat software as special in any way. Reverse engineering: You effectively reverse engineer a book when you read, study, and analyze its plot, characters, and theme. Grade school students reverse engineer stories all the time. Running private servers: There is no real prohibition on running a private server. You can run private servers all the time. The major case against private servers (BnetD) was because BnetD allowed unauthorized copies to play (a DMCA thing), and that a no-reverse engineering clause was violated on the terms of service (ToS) for BattleNet. But the court didn't rule that the concept of running private servers itself was illegal. [Note: The ToS is fundamentally different than the software EULA. You can still "own" the software but when you connect to BattleNet, you still would have to abide by their ToS since you don't own BattleNet.] Sale of used programs: The sale of used programs IS currently mandated and not under the discretion of the copyright holder. I don't know who told you that the copyright holder has the right to control the secondary market... but they can't. Trust me, if they could, they would-- every sale of a used copy of a game at Gamestop "deprives" the copyright holder of a sale of a new copy of the same software title, even though we somehow don't call this "piracy".
Publishers should not get to "avoid getting exploited by copyright law" if they benefit from the protection of copyright law. The purpose of copyright is to provide an incentive to create and ultimately benefit the general public. It isn't to protect or enrich a copyright holder. A software publisher or any other copyright holder might not like parts of copyright law, but those parts are in there for good reasons and contracts shouldn't be able to take those rights away.
There are fundamental differences between analysing a story and cracking a game. One is intended to be done (by good writers, anyway) and the other is not. Much of the value of a book lies in analysing the different levels on which the story works, and how different themes are portrayed. On the other hand, cracking the security features of a program is not necessary for it to be used as intended. It is generally only necessary when one is attempting something prohibited by copyright.
Running private servers: the unauthorized copy problem would exist on any private server, unless the person running it also duplicated the legitimate server's authorization processes and had a comprehensive list of authorized copies. That's extremely unlikely to ever happen. You DO see private servers, but some games allow them. I've seen games that actively encouraged them. That doesn't mean it's legal to do so without the copyright holder's permission.
I see you belong to the "EULAs aren't valid" school. If the software was owned instead of licensed, what you said about resale would be true. But since the consumer does not own the software, the publisher retains resale rights. If this were not true, every person who bought a game that prevents full resale (basically, any DRM you can think of, including Stardock's) could and should sue. And yes, in the context of software, selling used copies can often qualify as piracy. Most people don't think of it as such, but it can be, depending on how the license is written. For example, Blizzard explicitly ALLOWS resale for Diablo II, but not for WoW.
The purpose of copyright is to provide an incentive to create and ultimately benefit the general public. It isn't to protect or enrich a copyright holder.
And the incentive provided is mostly monetary. Yes, public recognition, professional standing, bragging rights, etc. are all protected by copyright, but the main force behind it is allowing the creator to sell his work without competition from people simply reprinting his work.
Lastly, reverse engineering is not an "evil" practice of thieves, but rather it is a standard engineering methodology. Medical science has been trying to reverse engineer the human body for centuries. A grade school student effectively reverse engineers a (copyrighted) story when he/she reads, studies, and analyzes the elements of the story. I think reverse engineering for ANY reason should be legal, whether it is to figure out how to improve something, or defeat a limitation (such as a copy protection scheme), or even to create a competing product. No one has really provided a justification why software needs or deserves any special protection from reverse engineering compared with other types of works.
I'd really like not to repeat the game cheats are illegal? discussion, but the basics are this: in no other form of media can one person reverse engineering a product affect the usability of someone else's copy of that product. Hacking the security system of a game to your benefit inevitably damages the usability of that product for others.
I might add that reverse engineering for purposes of creating competing products is generally breaking copyright (or patent, as is more common). That's the major reason patent rights run out so much faster than copyright - REing a physical object is often the first step in creating a (newly legal) competing product.