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 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.
This excludes that vast majority including over 98% of desktop / laptop computers running propriety Microsoft Windows or OS X
Since when do people not get root access on OSX or have control of their system? Sure Apple has a walled garden with gatekeeper and AMFI by default, a user can override this if they wish. It's not really DRM as much as it is codesigning enforcement.
All coins are of course vulnerable to botnet mining, CPU coins especially so. The largest XMR miner on minergate, botnet also. There are numerous ones mining XMR, and more will come for sure as the coin increases in value & exposure. I don't see it as huge issue personally, botherder tend to dump regularly instead of hoard. In some cases the market will feel no impact, because smart accumulator comes along with some webmoney to speak with, for all he knows is a AWS miner. Trying (and failing) to relegate CPU/GPU PoW on 'gnu/linux' than windows won't fix anything in long-term and it simply creates an uneven playing field and diminishes the user base