I am going to focus on the botnet issue because it is the only valid criticism I have seen of XMR among pages and pages of anti XMR posts. As fluffypony has correctly pointed out above virtually every POW coin and all POS coins are vulnerable to this. The notable exceptions at this point is XBT, and coins such as NMC that are merged mined with XBT
because of ASIC mining. To understand and deal with this issue we must go to the root cause and recognize a fundamental flaw in distributed crypto currency models:
The false assumption that most people particularly consumers actually control their computing devices
The only people that have real control are those who run a FLOSS operating system such as GNU/Linux or Android/Linux and have root access to their computer or device. This excludes that vast majority including over 98% of desktop / laptop computers running propriety Microsoft Windows or OS X and almost all mobile devices with the exception of rooted Android or some GNU/Linux based devices. There are two kinds of attacks here:
1) DRM based attacks. In this scenario the operating system vendor uses the DRM built into a propriety operating system to attack the coin. Since all popular propriety operating systems are infected with DRM this kind of attack can happen any time, either by the OS vendor on their own accord or at the request of a government actor. The best example of this is the attack by Apple on XBT since XBT's inception in 2009 until earlier this year on the Apple IOS platform.
2) Malware / botnet based attacks. These are most common on Microsoft Windows since this OS is particularly vulnerable to malware. The reasons behind this are beyond this discussion.
The solution here is to move the functions critical to the security of a coin away from DRM infected propriety operating systems such as Microsoft Windows to FLOSS operating systems such as GNU/Linux. In particular with a POW coin this means mining. This can be accomplished in a CPU / GPU coin by developing, releasing and supporting mining software only on GNU/Linux, and even going as far as avoiding cross platform development tools for the mining components. Making the mining software highly optimized for GNU/Linux. Targeting the ARM platform for mining is also a possibility. The idea is to make mining the coin far more efficient on GNU/Linux than on Microsoft Windows thereby putting botnets at a significant disadvantage.